Pierrick Roger
| Snapshot Date: 2024-07-22 14:00 -0400 (Mon, 22 Jul 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 2024-07-23 11:38 -0400 (Tue, 23 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4688 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4280 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4455 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4404 |
| 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 200/2248 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.11.0 (landing page) Pierrick Roger
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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: 2024-07-22 21:20:33 -0400 (Mon, 22 Jul 2024) |
| EndedAt: 2024-07-22 21:22:44 -0400 (Mon, 22 Jul 2024) |
| EllapsedTime: 130.2 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 ‘/home/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 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 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 ‘/home/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 [2024-07-22 21:21:19.203][biodb::testContext]
biodb.INFO [2024-07-22 21:21:19.207][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-22 21:21:19.208][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-07-22 21:21:19.209][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-22 21:21:19.210][biodb::testContext]
biodb.INFO [2024-07-22 21:21:19.219][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-07-22 21:21:19.222][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-07-22 21:21:19.230][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-22 21:21:19.232][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-22 21:21:19.233][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-22 21:21:19.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.237][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-22 21:21:19.258][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-22 21:21:19.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.262][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-22 21:21:19.263][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-22 21:21:19.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.267][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-22 21:21:19.268][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-22 21:21:19.269][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-22 21:21:19.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.273][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-22 21:21:19.274][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-22 21:21:19.275][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-22 21:21:19.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.279][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-22 21:21:19.280][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-22 21:21:19.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.284][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-22 21:21:19.285][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-22 21:21:19.286][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-22 21:21:19.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.290][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-22 21:21:19.291][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-22 21:21:19.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.295][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-22 21:21:19.296][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-22 21:21:19.297][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-22 21:21:19.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.301][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-22 21:21:19.302][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-22 21:21:19.303][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-22 21:21:19.304][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-22 21:21:19.305][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-22 21:21:19.306][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-22 21:21:19.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.310][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-22 21:21:19.311][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-22 21:21:19.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.315][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-22 21:21:19.316][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-22 21:21:19.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.320][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-22 21:21:19.321][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-22 21:21:19.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.324][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-22 21:21:19.326][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-22 21:21:19.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.329][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-22 21:21:19.330][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-22 21:21:19.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.334][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-22 21:21:19.335][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-22 21:21:19.339][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-22 21:21:19.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.343][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-22 21:21:19.344][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-22 21:21:19.345][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-22 21:21:19.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.352][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-22 21:21:19.390][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-22 21:21:19.427][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-22 21:21:19.429][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-22 21:21:19.430][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-22 21:21:19.431][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-22 21:21:19.432][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-22 21:21:19.433][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-22 21:21:19.434][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-22 21:21:19.435][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-22 21:21:19.436][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-22 21:21:19.437][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-22 21:21:19.438][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-22 21:21:19.439][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-22 21:21:19.440][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:21:19.441][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-22 21:21:19.442][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-22 21:21:19.442][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-22 21:21:19.442][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-22 21:21:19.442][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-22 21:21:19.442][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-22 21:21:19.443][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-22 21:21:19.444][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:21:19.445][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:21:19.446][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-22 21:21:19.447][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:21:19.448][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:21:19.449][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-22 21:21:19.450][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:21:19.451][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-22 21:21:19.452][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-22 21:21:19.454][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-22 21:21:19.455][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:21:19.458][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-22 21:21:19.461][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-22 21:21:19.462][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-22 21:21:19.463][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-22 21:21:19.464][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-22 21:21:19.465][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-22 21:21:19.466][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-22 21:21:19.467][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-22 21:21:19.468][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-22 21:21:19.469][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-22 21:21:19.470][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-22 21:21:19.471][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-22 21:21:19.472][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-22 21:21:19.473][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-22 21:21:19.474][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:21:19.475][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-22 21:21:19.476][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-22 21:21:19.476][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-22 21:21:19.476][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-22 21:21:19.476][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-22 21:21:19.476][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-22 21:21:19.477][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-22 21:21:19.478][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:21:19.479][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:21:19.480][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-22 21:21:19.481][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:21:19.481][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:21:19.482][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-22 21:21:19.483][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:21:19.484][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-22 21:21:19.485][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-22 21:21:19.486][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-22 21:21:19.487][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:21:19.488][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-22 21:21:19.490][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-22 21:21:19.490][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-22 21:21:19.491][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-22 21:21:19.492][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-22 21:21:19.493][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-22 21:21:19.494][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-22 21:21:19.495][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-22 21:21:19.496][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-22 21:21:19.497][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-22 21:21:19.498][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-22 21:21:19.499][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-22 21:21:19.500][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-22 21:21:19.501][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-22 21:21:19.502][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:21:19.502][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-22 21:21:19.503][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:21:19.504][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-22 21:21:19.505][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:21:19.506][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:21:19.507][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-22 21:21:19.508][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:21:19.509][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:21:19.510][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-22 21:21:19.511][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:21:19.512][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-22 21:21:19.512][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-22 21:21:19.513][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-22 21:21:19.514][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:21:19.515][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-22 21:21:19.517][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-22 21:21:19.518][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-22 21:21:19.519][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-22 21:21:19.520][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-22 21:21:19.521][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-22 21:21:19.522][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-22 21:21:19.523][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-22 21:21:19.524][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-22 21:21:19.524][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-22 21:21:19.525][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-22 21:21:19.526][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-22 21:21:19.527][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-22 21:21:19.528][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-22 21:21:19.529][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:21:19.530][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-22 21:21:19.531][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:21:19.532][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-22 21:21:19.533][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:21:19.534][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:21:19.534][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-22 21:21:19.535][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:21:19.536][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:21:19.537][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-22 21:21:19.538][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:21:19.539][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-22 21:21:19.540][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-22 21:21:19.541][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-22 21:21:19.541][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:21:19.545][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-22 21:21:19.546][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.619][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-22 21:21:19.624][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-22 21:21:19.625][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-22 21:21:19.626][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-22 21:21:19.628][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-22 21:21:19.629][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-22 21:21:19.630][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-22 21:21:19.632][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-22 21:21:19.633][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-22 21:21:19.634][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-22 21:21:19.635][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-22 21:21:19.637][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-22 21:21:19.638][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-22 21:21:19.639][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-22 21:21:19.641][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-22 21:21:19.642][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-22 21:21:19.643][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-22 21:21:19.645][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-22 21:21:19.646][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-22 21:21:19.647][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-22 21:21:19.649][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-22 21:21:19.650][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-22 21:21:19.651][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-22 21:21:19.653][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-22 21:21:19.654][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-22 21:21:19.655][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-22 21:21:19.657][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-22 21:21:19.658][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-22 21:21:19.659][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-22 21:21:19.660][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-22 21:21:19.662][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-22 21:21:19.663][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-22 21:21:19.665][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-22 21:21:19.666][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-22 21:21:19.667][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-22 21:21:19.669][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-22 21:21:19.675][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-22 21:21:19.676][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-22 21:21:19.677][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-22 21:21:19.678][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-22 21:21:19.680][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-22 21:21:19.681][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-22 21:21:19.682][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-22 21:21:19.684][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-22 21:21:19.685][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-22 21:21:19.686][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-22 21:21:19.687][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-22 21:21:19.689][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-22 21:21:19.690][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-22 21:21:19.691][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-22 21:21:19.693][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-22 21:21:19.694][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-22 21:21:19.695][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-22 21:21:19.696][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-22 21:21:19.698][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-22 21:21:19.699][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-22 21:21:19.700][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-22 21:21:19.702][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-22 21:21:19.703][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-22 21:21:19.704][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-22 21:21:19.705][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-22 21:21:19.707][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-22 21:21:19.708][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-22 21:21:19.709][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-22 21:21:19.711][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-22 21:21:19.712][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-22 21:21:19.713][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-22 21:21:19.714][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-22 21:21:19.716][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-22 21:21:19.717][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-22 21:21:19.718][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-22 21:21:19.720][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-22 21:21:19.721][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-22 21:21:19.722][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-22 21:21:19.723][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-22 21:21:19.725][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-22 21:21:19.726][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-22 21:21:19.727][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-22 21:21:19.729][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-22 21:21:19.730][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-22 21:21:19.731][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-22 21:21:19.732][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-22 21:21:19.734][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-22 21:21:19.739][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-22 21:21:19.741][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-07-22 21:21:19.744][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-22 21:21:19.745][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.746][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:19.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:19.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:19.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:19.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:19.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:19.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:19.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:19.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:19.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:19.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:19.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:19.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.786][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[2024-07-22 21:21:19.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:19.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:19.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:19.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:19.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:19.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:19.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:19.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:19.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:19.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:19.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.815][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[2024-07-22 21:21:19.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:19.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:19.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:19.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:19.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:19.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:19.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.832][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[2024-07-22 21:21:19.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:19.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:19.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:19.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:19.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:19.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:21:19.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:19.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:19.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.849][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[2024-07-22 21:21:19.851][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-07-22 21:21:19.860][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-07-22 21:21:19.862][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-22 21:21:19.863][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-22 21:21:19.864][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-22 21:21:19.865][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-22 21:21:19.866][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-22 21:21:19.867][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-22 21:21:19.868][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-22 21:21:19.869][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-07-22 21:21:19.870][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-07-22 21:21:19.870][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-22 21:21:19.871][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-22 21:21:19.872][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-07-22 21:21:19.873][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-22 21:21:19.874][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-07-22 21:21:19.874][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-07-22 21:21:19.874][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-07-22 21:21:19.874][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-07-22 21:21:19.874][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-07-22 21:21:19.874][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-07-22 21:21:19.874][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-07-22 21:21:19.874][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-07-22 21:21:19.874][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-07-22 21:21:19.874][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-07-22 21:21:19.874][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-07-22 21:21:19.875][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-22 21:21:19.876][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-22 21:21:19.876][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-22 21:21:19.876][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-22 21:21:19.877][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-22 21:21:19.878][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:21:19.879][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:21:19.880][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-22 21:21:19.881][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:21:19.882][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:21:19.882][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-22 21:21:19.883][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-22 21:21:19.883][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-07-22 21:21:19.884][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-22 21:21:19.885][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-22 21:21:19.886][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-22 21:21:19.887][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-07-22 21:21:19.887][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-07-22 21:21:19.893][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-22 21:21:19.894][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-22 21:21:19.896][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-07-22 21:21:19.897][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-22 21:21:19.899][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-22 21:21:19.900][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-22 21:21:19.928][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-07-22 21:21:19.929][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-07-22 21:21:19.934][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-07-22 21:21:19.938][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-07-22 21:21:19.943][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-22 21:21:19.944][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-22 21:21:19.945][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-07-22 21:21:19.946][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-07-22 21:21:19.956][biodb::testThat]
biodb.INFO [2024-07-22 21:21:19.957][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-07-22 21:21:19.958][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-22 21:21:19.959][biodb::testThat]
biodb.TRACE[2024-07-22 21:21:19.962][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-07-22 21:21:19.964][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-22 21:21:19.968][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-22 21:21:19.977][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:19.978][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:19.979][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:19.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:19.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:19.994][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:19.995][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[2024-07-22 21:21:20.005][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:20.006][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:20.007][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.008][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:20.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:20.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.025][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:20.026][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:20.027][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.028][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.053][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:20.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:20.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.057][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:20.058][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:20.059][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.060][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.061][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:20.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:20.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.065][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:20.066][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:20.067][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.068][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.069][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:20.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:20.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.073][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:20.074][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:20.075][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.076][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.077][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:20.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:20.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.081][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:20.082][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:20.083][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.084][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.085][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:20.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:20.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.089][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:20.090][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:20.091][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.092][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.093][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:20.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:20.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.097][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:20.098][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:20.099][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.100][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.101][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:20.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:20.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.105][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:20.106][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:20.107][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.107][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.109][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:20.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:20.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.113][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:20.114][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:20.115][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.115][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.117][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:20.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:20.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.121][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:20.122][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:20.122][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.123][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.125][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:20.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:20.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.129][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:20.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:20.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.132][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:20.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:20.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:20.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:20.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.140][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:20.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:20.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:20.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:20.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:20.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:20.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:20.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:20.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:20.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:20.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:20.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:20.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:20.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:20.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:20.209][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-07-22 21:21:20.212][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:20.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:20.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.215][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:20.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:20.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.241][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:20.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:20.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.245][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:20.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:20.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.249][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:20.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:20.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.252][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:20.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:20.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.256][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-22 21:21:20.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-22 21:21:20.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.260][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-22 21:21:20.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-22 21:21:20.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.263][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-22 21:21:20.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-22 21:21:20.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.267][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-22 21:21:20.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-22 21:21:20.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.287][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:20.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:20.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.302][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:20.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:20.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:20.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:20.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:20.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:20.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:20.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:20.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:20.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:20.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:20.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:20.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:20.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:20.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.334][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:20.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:20.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.338][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:20.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:20.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.342][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:20.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:20.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:20.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:20.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:20.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:20.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:20.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:20.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.363][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:20.364][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:20.365][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.366][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:20.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:20.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:20.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:20.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.412][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:20.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:20.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.416][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:20.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:20.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.420][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:20.421][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:20.422][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.423][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.424][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:20.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:20.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.435][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:20.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:20.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.439][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:20.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:20.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.443][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:20.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:20.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.447][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:20.448][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:20.449][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.450][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.451][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:20.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:20.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.462][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:20.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:20.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.466][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:20.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:20.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.469][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:20.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:20.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.473][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:20.474][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:20.475][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.476][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.477][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:20.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:20.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.488][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:20.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:20.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.492][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:20.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:20.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.495][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:20.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:20.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.499][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:20.500][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:20.501][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.502][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.503][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:20.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:20.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.514][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:20.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:20.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.518][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:20.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:20.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.522][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:20.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:20.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.526][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:20.527][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:20.528][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.529][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.530][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:20.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:20.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.541][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:20.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:20.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.545][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:20.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:20.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.549][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:20.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:20.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.553][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:20.554][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:20.555][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.556][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.557][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:20.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:20.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.568][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-07-22 21:21:20.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:20.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.572][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-07-22 21:21:20.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:20.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.576][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-07-22 21:21:20.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:20.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.580][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-07-22 21:21:20.581][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:20.582][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.582][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.583][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-07-22 21:21:20.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:20.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.595][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:20.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:20.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.599][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:20.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:20.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.603][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:20.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:20.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.607][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:20.608][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:20.609][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.610][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.611][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:20.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:20.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.622][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:20.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:20.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.627][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:20.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:20.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.637][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:20.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:20.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.641][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:20.642][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:20.642][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.643][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.644][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:20.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:20.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.656][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:20.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:20.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.660][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:20.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:20.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.664][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:20.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:20.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.668][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:20.669][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:20.670][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.671][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.672][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:20.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:20.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.682][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:20.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:20.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.686][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:20.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:20.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.690][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:20.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:20.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.693][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:20.694][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:20.695][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.696][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.697][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:20.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:20.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.708][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:20.709][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:20.710][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.711][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.715][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:20.716][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:20.717][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.718][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.721][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:20.722][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:20.723][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.724][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.728][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:20.729][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:20.730][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.731][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.735][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:20.736][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:20.737][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.738][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.742][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:20.743][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:20.744][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.744][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.748][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:20.749][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:20.750][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.751][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.755][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:20.756][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:20.757][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.758][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.762][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-07-22 21:21:20.763][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:20.764][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.765][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.769][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:20.770][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:20.771][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.772][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.776][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:20.777][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:20.778][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.779][ef$get] fields variable is a list.
biodb.INFO [2024-07-22 21:21:20.785][biodb::testThat]
biodb.INFO [2024-07-22 21:21:20.786][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-07-22 21:21:20.787][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-22 21:21:20.788][biodb::testThat]
biodb.DEBUG[2024-07-22 21:21:20.801][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-07-22 21:21:20.809][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-22 21:21:20.814][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-07-22 21:21:20.815][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-22 21:21:20.816][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-07-22 21:21:20.817][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-22 21:21:20.846][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-22 21:21:20.847][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-22 21:21:20.849][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:20.850][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:20.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:20.855][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:20.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:20.857][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:20.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:20.860][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:20.861][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:20.862][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.863][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:20.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:20.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.884][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:20.886][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:20.887][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.888][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.889][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:20.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:20.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.893][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:20.894][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:20.895][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.896][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.897][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:20.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:20.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.901][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:20.902][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:20.903][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.904][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.905][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:20.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:20.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.909][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:20.910][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:20.911][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.912][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.913][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:20.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:20.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.917][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:20.918][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:20.919][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.920][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.921][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:20.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:20.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.925][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:20.926][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:20.927][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.927][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.929][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:20.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:20.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.933][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:20.934][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:20.934][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.935][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.937][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:20.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:20.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.940][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:20.941][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:20.942][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.943][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.945][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:20.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:20.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.949][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:20.950][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:20.950][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.951][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.953][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:20.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:20.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.957][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:20.957][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:20.958][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.959][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.961][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:20.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:20.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.965][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:20.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:20.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.968][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:20.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:20.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:20.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:20.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.976][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:20.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:20.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:20.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:20.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:20.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:20.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:20.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:20.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:20.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:20.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:20.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:20.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:20.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:20.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:21.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:21.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:21.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:21.003][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-07-22 21:21:21.004][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-07-22 21:21:21.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-07-22 21:21:21.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:21.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:21.008][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-07-22 21:21:21.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-07-22 21:21:21.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:21.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:21.012][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-07-22 21:21:21.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-07-22 21:21:21.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:21.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-22 21:21:21.022][biodb::testThat]
biodb.INFO [2024-07-22 21:21:21.024][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-07-22 21:21:21.025][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-22 21:21:21.025][biodb::testThat]
biodb.TRACE[2024-07-22 21:21:21.029][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:21.030][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:21.031][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:21.032][ef$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:21.033][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-07-22 21:21:21.062][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:21.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:21.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:21.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:21.067][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:21.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:21.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:21.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:21.071][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:21.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:21.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:21.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:21.078][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-07-22 21:21:21.083][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-07-22 21:21:21.104][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-22 21:21:21.119][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-07-22 21:21:21.121][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-22 21:21:21.122][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-07-22 21:21:21.144][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[2024-07-22 21:21:21.147][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:21:21.148][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:21:21.150][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-22 21:21:21.824][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-22 21:21:22.394][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:21:22.396][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-07-22 21:21:22.412][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-07-22 21:21:22.415][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-07-22 21:21:22.427][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:22.428][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:22.429][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:22.430][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:22.431][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:22.432][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:22.433][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:22.434][ef$get] fields variable is a list.
biodb.INFO [2024-07-22 21:21:22.438][biodb::testThat]
biodb.INFO [2024-07-22 21:21:22.439][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-07-22 21:21:22.440][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-22 21:21:22.441][biodb::testThat]
biodb.TRACE[2024-07-22 21:21:22.466][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:22.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:22.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:22.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:22.471][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:22.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:22.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:22.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:22.475][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:22.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:22.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:22.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:22.532][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-22 21:21:22.536][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-22 21:21:22.537][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-07-22 21:21:22.538][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-22 21:21:22.540][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-07-22 21:21:22.555][biodb::testThat]
biodb.INFO [2024-07-22 21:21:22.556][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-07-22 21:21:22.557][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-22 21:21:22.558][biodb::testThat]
biodb.TRACE[2024-07-22 21:21:22.589][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:22.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:22.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:22.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:22.594][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:22.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:22.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:22.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:22.598][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:22.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:22.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:22.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:22.602][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:22.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:22.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:22.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:22.606][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:22.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:22.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:22.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:22.610][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:22.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:22.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:22.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:22.614][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-22 21:21:22.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-22 21:21:22.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:22.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:22.618][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-22 21:21:22.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-22 21:21:22.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:22.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:22.622][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-22 21:21:22.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-22 21:21:22.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:22.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:22.626][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-22 21:21:22.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-22 21:21:22.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:22.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:22.648][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:22.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:22.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:22.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:22.653][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:22.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:22.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:22.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:22.658][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:22.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:22.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:22.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:22.663][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:22.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:22.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:22.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:22.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:22.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:22.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:22.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:22.670][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:22.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:22.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:22.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:22.674][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-22 21:21:22.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-22 21:21:22.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:22.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:22.678][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-22 21:21:22.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-22 21:21:22.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:22.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:22.682][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-22 21:21:22.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-22 21:21:22.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:22.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:22.686][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-22 21:21:22.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-22 21:21:22.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:22.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-22 21:21:22.696][biodb::testThat]
biodb.INFO [2024-07-22 21:21:22.697][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-07-22 21:21:22.698][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-22 21:21:22.699][biodb::testThat]
biodb.INFO [2024-07-22 21:21:22.708][biodb::testThat]
biodb.INFO [2024-07-22 21:21:22.710][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-07-22 21:21:22.711][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-22 21:21:22.712][biodb::testThat]
biodb.INFO [2024-07-22 21:21:22.721][biodb::testThat]
biodb.INFO [2024-07-22 21:21:22.722][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-07-22 21:21:22.723][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-22 21:21:22.724][biodb::testThat]
biodb.DEBUG[2024-07-22 21:21:22.727][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-07-22 21:21:23.278][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-07-22 21:21:24.414][biodb::testThat]
biodb.INFO [2024-07-22 21:21:24.416][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-07-22 21:21:24.418][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-22 21:21:24.420][biodb::testThat]
biodb.DEBUG[2024-07-22 21:21:24.872][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[2024-07-22 21:21:25.313][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:25.316][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:25.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:25.320][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:25.323][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:25.325][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:25.327][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:25.329][ef$get] fields variable is a list.
biodb.INFO [2024-07-22 21:21:25.333][biodb::testThat]
biodb.INFO [2024-07-22 21:21:25.335][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2024-07-22 21:21:25.354][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-22 21:21:25.356][biodb::testThat]
biodb.TRACE[2024-07-22 21:21:25.372][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:25.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:25.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:25.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:25.377][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:25.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:25.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:25.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:25.382][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:25.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:25.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:25.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:25.484][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-22 21:21:25.488][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-22 21:21:25.489][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-07-22 21:21:25.491][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-22 21:21:25.492][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-07-22 21:21:25.555][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-22 21:21:25.559][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-22 21:21:25.560][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-07-22 21:21:25.573][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-22 21:21:25.575][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-07-22 21:21:25.589][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-22 21:21:25.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-22 21:21:25.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:25.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:25.597][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:25.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:25.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:25.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:25.601][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:25.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:25.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:25.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:25.605][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:25.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:25.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:25.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:25.608][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:25.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:25.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:25.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:25.612][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:25.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:25.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:25.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:25.623][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-22 21:21:25.639][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:21:25.640][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:21:25.655][private$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[2024-07-22 21:21:26.042][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[2024-07-22 21:21:26.465][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:21:26.469][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-07-22 21:21:26.478][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-07-22 21:21:26.484][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:26.486][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:26.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:26.498][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:26.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:26.502][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:26.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:26.507][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-07-22 21:21:26.568][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-22 21:21:26.570][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-07-22 21:21:26.571][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-22 21:21:26.572][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-22 21:21:26.578][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-22 21:21:26.582][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-22 21:21:26.583][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-22 21:21:26.584][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-22 21:21:26.587][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:26.588][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:26.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:26.593][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:26.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:26.595][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:26.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:26.597][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-07-22 21:21:26.599][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:21:26.600][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:21:26.601][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-07-22 21:21:26.987][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-07-22 21:21:27.419][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:21:27.423][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-07-22 21:21:27.430][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-07-22 21:21:27.436][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-07-22 21:21:27.439][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-22 21:21:27.441][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-22 21:21:27.444][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-22 21:21:27.447][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:27.449][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:27.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:27.461][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:27.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:27.464][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:27.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:27.470][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:27.472][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:27.473][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:27.475][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:27.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:27.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:27.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:27.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:27.483][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:27.484][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:27.486][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:27.487][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:27.516][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:27.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:27.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:27.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:27.520][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:27.522][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:27.523][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:27.523][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:27.525][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:27.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:27.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:27.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:27.529][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:27.530][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:27.531][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:27.532][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:27.533][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:27.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:27.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:27.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:27.537][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:27.538][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:27.539][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:27.539][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:27.541][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:27.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:27.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:27.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:27.544][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:27.545][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:27.546][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:27.547][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:27.548][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:27.549][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:27.550][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:27.551][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:27.552][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:27.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:27.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:27.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:27.556][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:27.557][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:27.558][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:27.558][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:27.560][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:27.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:27.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:27.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:27.563][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:27.564][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:27.565][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:27.566][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:27.567][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:27.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:27.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:27.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:27.571][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:27.572][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:27.573][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:27.574][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:27.575][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:27.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:27.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:27.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:27.579][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:27.580][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:27.581][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:27.582][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:27.583][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:27.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:27.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:27.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:27.587][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:27.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:27.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:27.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:27.590][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:27.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:27.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:27.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:27.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:27.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:27.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:27.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:27.606][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:27.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:27.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:27.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:27.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:27.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:27.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:27.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:27.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:27.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:27.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:27.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:27.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:27.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:27.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:27.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:27.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:27.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:27.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:27.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:27.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:27.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:27.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:27.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:27.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:27.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:27.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:27.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:27.632][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-07-22 21:21:27.641][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:27.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:27.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:27.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:27.645][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:27.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:27.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:27.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:27.649][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:27.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:27.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:27.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:27.654][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[2024-07-22 21:21:27.657][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:21:27.658][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:21:27.659][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-22 21:21:28.045][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-22 21:21:28.441][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:21:28.445][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-07-22 21:21:28.453][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-07-22 21:21:28.487][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:28.488][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:28.490][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:28.497][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:28.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:28.500][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:28.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:28.503][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:28.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:28.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:28.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:28.509][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:28.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:28.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:28.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:28.514][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:28.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:28.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:28.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:28.519][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:28.520][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:28.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:28.526][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:28.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:28.528][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:28.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:28.530][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-07-22 21:21:28.531][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-22 21:21:28.532][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-07-22 21:21:28.533][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-22 21:21:28.535][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-22 21:21:28.536][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-22 21:21:28.537][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-22 21:21:28.537][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-22 21:21:28.538][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-22 21:21:28.551][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:28.552][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:28.553][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:28.558][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:28.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:28.559][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:28.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:28.561][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-07-22 21:21:28.564][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:21:28.565][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:21:28.566][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-07-22 21:21:28.953][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-07-22 21:21:29.391][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:21:29.402][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-07-22 21:21:29.456][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-07-22 21:21:29.460][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-07-22 21:21:29.461][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-22 21:21:29.463][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-22 21:21:29.465][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-22 21:21:29.467][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:29.468][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:29.469][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:29.474][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:29.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:29.477][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:29.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:29.480][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:29.481][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:29.482][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.483][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:29.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:29.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:29.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:29.489][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:29.490][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:29.491][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.492][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:29.493][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:29.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:29.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:29.497][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:29.498][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:29.499][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.500][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:29.501][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:29.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:29.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:29.506][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:29.507][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:29.508][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.508][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:29.510][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:29.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:29.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:29.514][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:29.515][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:29.516][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.517][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:29.518][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:29.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:29.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:29.522][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:29.523][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:29.524][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.525][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:29.526][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:29.527][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:29.528][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.529][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:29.531][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:29.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:29.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:29.535][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:29.536][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:29.537][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.538][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:29.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:29.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:29.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:29.543][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:29.544][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:29.545][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.546][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:29.548][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:29.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:29.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:29.552][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:29.553][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:29.554][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.554][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:29.556][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:29.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:29.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:29.560][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:29.561][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:29.562][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.563][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:29.564][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:29.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:29.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:29.568][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:29.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:29.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:29.572][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:29.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:29.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:29.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:29.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:29.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:29.580][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:29.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:29.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:29.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:29.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:29.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:29.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:29.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:29.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:29.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:29.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:29.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:29.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:29.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:29.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:29.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:29.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:29.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:29.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:29.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:29.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:29.608][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-07-22 21:21:29.609][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:29.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:29.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:29.613][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:29.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:29.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:29.617][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:29.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:29.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:29.643][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-22 21:21:29.646][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-22 21:21:29.648][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-07-22 21:21:29.649][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-22 21:21:29.650][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-07-22 21:21:29.653][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:29.654][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:29.655][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:29.659][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:29.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:29.661][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:29.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:29.663][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:29.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:29.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:29.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:29.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:29.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:29.670][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:29.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:29.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:29.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:29.674][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:29.675][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:29.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:29.680][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:29.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:29.682][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:29.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:29.683][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-07-22 21:21:29.684][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-22 21:21:29.686][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-07-22 21:21:29.687][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-22 21:21:29.688][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-22 21:21:29.689][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-22 21:21:29.690][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-22 21:21:29.691][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-22 21:21:29.692][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-22 21:21:29.694][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:29.695][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:29.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:29.700][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:29.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:29.702][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:29.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:29.704][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-07-22 21:21:29.706][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:21:29.707][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:21:29.709][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-07-22 21:21:30.095][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-07-22 21:21:30.515][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:21:30.518][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-07-22 21:21:30.523][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-07-22 21:21:30.528][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-07-22 21:21:30.530][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-22 21:21:30.532][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-22 21:21:30.534][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-22 21:21:30.536][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:30.538][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:30.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:30.547][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:30.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:30.550][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:30.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:30.555][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:30.557][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:30.558][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:30.560][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:30.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:30.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:30.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:30.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:30.567][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:30.569][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:30.570][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:30.571][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:30.573][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:30.574][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:30.575][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:30.577][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:30.578][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:30.580][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:30.581][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:30.582][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:30.583][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:30.584][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:30.585][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:30.586][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:30.587][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:30.589][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:30.590][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:30.590][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:30.592][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:30.593][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:30.594][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:30.595][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:30.596][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:30.597][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:30.598][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:30.599][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:30.600][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:30.601][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:30.601][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:30.602][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:30.604][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:30.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:30.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:30.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:30.607][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:30.608][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:30.609][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:30.610][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:30.611][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:30.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:30.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:30.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:30.615][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:30.616][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:30.617][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:30.618][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:30.619][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:30.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:30.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:30.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:30.622][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:30.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:30.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:30.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:30.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:30.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:30.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:30.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:30.630][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:30.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:30.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:30.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:30.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:30.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:30.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:30.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:30.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:30.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:30.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:30.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:30.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:30.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:30.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:30.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:30.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:30.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:30.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:30.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:30.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:30.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:30.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:30.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:30.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:30.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:30.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:30.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:30.664][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-07-22 21:21:30.665][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:30.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:30.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:30.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:30.669][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:30.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:30.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:30.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:30.673][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:30.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:30.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:30.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:30.676][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:30.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:30.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:30.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:30.680][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:30.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:30.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:30.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:30.684][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:30.685][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:30.686][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:30.690][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:30.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:30.692][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:30.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:30.693][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-07-22 21:21:30.694][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-22 21:21:30.696][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-07-22 21:21:30.697][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-22 21:21:30.698][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-22 21:21:30.699][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-22 21:21:30.700][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-22 21:21:30.701][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-22 21:21:30.702][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-22 21:21:30.704][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:30.705][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:30.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:30.710][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:30.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:30.712][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:30.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:30.714][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-07-22 21:21:30.717][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:21:30.717][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:21:30.719][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-07-22 21:21:31.107][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-07-22 21:21:31.501][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:21:31.505][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-07-22 21:21:31.512][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-07-22 21:21:31.518][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-07-22 21:21:31.521][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-22 21:21:31.524][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-22 21:21:31.526][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-22 21:21:31.530][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:31.532][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:31.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:31.543][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:31.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:31.546][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:31.548][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.TRACE[2024-07-22 21:21:31.552][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:31.553][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:31.555][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:31.556][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:31.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:31.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:31.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:31.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:31.564][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:31.566][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:31.567][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:31.568][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:31.570][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:31.571][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:31.573][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:31.574][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:31.575][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:31.577][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:31.578][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:31.579][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:31.580][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:31.581][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:31.582][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:31.583][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:31.585][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:31.586][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:31.587][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:31.588][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:31.589][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:31.590][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:31.591][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:31.592][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:31.593][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:31.594][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:31.595][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:31.596][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:31.597][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:31.598][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:31.599][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:31.600][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:31.601][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:31.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:31.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:31.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:31.605][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:31.606][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:31.607][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:31.608][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:31.609][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:31.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:31.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:31.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:31.613][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:31.614][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:31.615][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:31.615][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:31.617][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:31.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:31.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:31.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:31.620][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:31.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:31.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:31.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:31.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:31.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:31.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:31.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:31.637][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:31.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:31.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:31.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:31.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:31.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:31.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:31.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:31.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:31.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:31.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:31.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:31.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:31.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:31.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:31.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:31.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:31.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:31.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:31.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:31.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:31.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:31.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:31.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:31.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:31.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:31.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:31.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:31.662][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-07-22 21:21:31.663][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:31.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:31.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:31.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:31.667][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:31.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:31.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:31.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:31.671][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:31.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:31.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:31.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:31.674][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:31.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:31.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:31.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:31.678][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:31.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:31.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:31.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:31.682][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:31.683][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:31.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:31.688][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:31.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:31.690][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:31.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:31.692][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-07-22 21:21:31.693][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-22 21:21:31.694][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-07-22 21:21:31.695][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-22 21:21:31.696][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-22 21:21:31.697][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-22 21:21:31.698][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-22 21:21:31.699][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-22 21:21:31.700][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-22 21:21:31.703][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:31.704][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:31.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:31.709][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:31.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:31.710][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:31.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:31.712][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-07-22 21:21:31.715][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:21:31.716][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:21:31.717][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-07-22 21:21:32.106][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-07-22 21:21:32.529][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:21:32.534][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-07-22 21:21:32.541][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-07-22 21:21:32.546][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-07-22 21:21:32.549][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-22 21:21:32.552][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-22 21:21:32.554][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-22 21:21:32.558][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:32.560][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:32.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:32.571][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:32.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:32.574][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:32.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:32.580][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:32.582][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:32.583][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:32.585][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:32.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:32.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:32.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:32.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:32.592][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:32.594][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:32.595][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:32.596][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:32.598][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:32.600][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:32.601][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:32.602][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:32.604][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:32.605][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:32.606][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:32.607][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:32.608][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:32.609][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:32.610][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:32.611][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:32.613][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:32.614][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:32.615][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:32.616][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:32.617][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:32.618][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:32.619][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:32.620][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:32.621][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:32.622][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:32.623][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:32.624][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:32.625][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:32.626][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:32.626][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:32.627][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:32.629][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:32.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:32.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:32.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:32.633][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:32.634][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:32.634][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:32.635][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:32.636][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:32.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:32.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:32.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:32.645][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:32.649][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:32.650][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:32.651][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:32.652][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:32.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:32.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:32.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:32.655][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:32.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:32.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:32.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:32.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:32.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:32.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:32.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:32.663][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:32.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:32.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:32.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:32.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:32.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:32.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:32.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:32.670][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:32.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:32.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:32.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:32.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:32.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:32.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:32.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:32.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:32.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:32.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:32.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:32.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:32.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:32.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:32.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:32.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:32.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:32.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:32.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:32.689][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-07-22 21:21:32.690][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:32.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:32.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:32.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:32.693][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:32.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:32.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:32.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:32.697][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:32.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:32.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:32.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:32.701][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:32.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:32.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:32.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:32.704][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:32.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:32.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:32.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:32.708][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:32.709][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:32.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:32.714][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:32.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:32.716][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:32.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:32.718][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-07-22 21:21:32.719][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-22 21:21:32.720][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-07-22 21:21:32.721][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-22 21:21:32.722][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-22 21:21:32.723][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-22 21:21:32.724][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-22 21:21:32.725][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-22 21:21:32.726][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-22 21:21:32.729][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:32.730][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:32.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:32.735][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:32.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:32.736][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:32.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:32.738][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-07-22 21:21:32.741][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:21:32.742][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:21:32.743][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-07-22 21:21:33.130][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-07-22 21:21:33.564][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:21:33.569][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-07-22 21:21:33.576][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-07-22 21:21:33.581][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-07-22 21:21:33.584][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-22 21:21:33.587][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-22 21:21:33.590][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-22 21:21:33.593][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:33.595][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:33.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:33.618][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:33.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:33.621][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:33.623][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.TRACE[2024-07-22 21:21:33.628][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:33.630][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:33.631][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.632][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:33.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:33.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:33.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:33.640][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:33.641][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:33.642][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.643][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:33.645][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:33.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:33.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:33.650][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:33.651][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:33.652][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.653][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:33.655][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:33.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:33.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:33.659][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:33.660][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:33.661][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.662][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:33.663][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:33.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:33.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:33.668][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:33.669][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:33.670][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.670][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:33.672][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:33.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:33.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:33.676][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:33.677][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:33.697][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.698][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:33.700][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:33.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:33.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:33.704][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:33.705][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:33.706][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.707][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:33.708][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:33.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:33.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:33.712][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:33.713][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:33.714][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.715][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:33.716][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:33.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:33.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:33.720][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:33.721][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:33.722][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.723][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:33.725][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:33.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:33.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:33.729][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:33.730][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:33.731][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.732][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:33.733][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:33.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:33.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:33.737][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:33.738][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:33.739][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.740][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:33.741][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:33.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:33.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:33.745][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:33.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:33.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:33.749][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:33.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:33.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:33.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:33.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:33.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:33.757][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:33.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:33.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:33.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:33.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:33.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:33.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:33.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:33.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:33.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:33.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:33.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:33.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:33.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:33.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:33.777][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:33.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:33.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:33.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:33.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:33.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:33.785][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-07-22 21:21:33.786][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:33.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:33.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:33.790][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:33.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:33.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:33.794][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:33.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:33.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:33.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:33.798][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:33.799][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:33.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:33.804][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:33.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:33.806][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:33.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:33.808][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-07-22 21:21:33.809][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-22 21:21:33.811][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-07-22 21:21:33.812][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-22 21:21:33.813][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-22 21:21:33.814][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-22 21:21:33.815][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-22 21:21:33.816][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-22 21:21:33.817][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-22 21:21:33.820][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:33.820][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:33.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:33.826][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:33.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:33.827][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:33.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:33.829][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-07-22 21:21:33.832][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:21:33.833][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:21:33.834][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-07-22 21:21:34.221][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-07-22 21:21:34.656][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:21:34.661][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-07-22 21:21:34.668][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-07-22 21:21:34.673][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-07-22 21:21:34.676][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-22 21:21:34.679][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-22 21:21:34.681][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-22 21:21:34.684][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:34.686][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:34.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:34.697][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:34.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:34.701][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:34.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:34.707][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:34.709][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:34.710][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.712][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:34.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:34.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:34.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:34.729][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:34.730][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:34.731][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.732][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:34.734][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:34.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:34.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:34.738][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:34.739][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:34.740][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.741][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:34.743][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:34.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:34.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:34.747][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:34.748][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:34.749][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.750][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:34.751][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:34.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:34.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:34.755][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:34.756][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:34.757][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.758][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:34.759][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:34.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:34.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:34.762][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:34.763][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:34.764][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.765][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:34.766][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:34.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:34.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:34.770][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:34.771][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:34.772][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.773][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:34.774][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:34.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:34.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:34.778][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:34.779][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:34.780][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.781][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:34.782][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:34.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:34.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:34.785][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:34.786][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:34.787][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.788][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:34.789][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:34.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:34.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:34.793][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:34.794][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:34.795][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.796][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:34.797][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:34.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:34.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:34.801][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:34.802][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:34.803][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.804][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:34.805][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:34.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:34.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:34.808][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:34.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:34.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:34.812][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:34.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:34.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:34.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:34.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:34.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:34.819][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:34.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:34.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:34.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:34.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:34.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:34.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:34.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:34.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:34.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:34.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:34.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:34.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:34.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:34.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:34.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:34.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:34.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:34.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:34.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:34.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:34.845][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-07-22 21:21:34.847][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:34.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:34.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:34.850][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:34.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:34.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:34.854][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:34.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:34.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:34.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:34.858][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:34.858][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:34.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:34.863][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:34.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:34.865][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:34.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:34.867][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-07-22 21:21:34.868][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-22 21:21:34.869][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-07-22 21:21:34.870][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-22 21:21:34.872][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-22 21:21:34.873][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-22 21:21:34.873][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-22 21:21:34.874][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-22 21:21:34.875][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-22 21:21:34.878][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:34.879][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:34.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:34.884][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:34.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:34.885][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:34.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:34.887][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-07-22 21:21:34.890][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:21:34.896][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:21:34.898][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-07-22 21:21:35.286][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-07-22 21:21:35.710][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:21:35.713][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-07-22 21:21:35.719][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-07-22 21:21:35.724][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-07-22 21:21:35.726][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-22 21:21:35.728][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-22 21:21:35.730][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-22 21:21:35.733][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:35.734][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:35.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:35.743][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:35.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:35.746][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:35.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:35.750][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:35.752][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:35.753][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:35.755][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:35.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:35.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:35.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:35.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:35.762][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:35.764][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:35.765][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:35.767][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:35.769][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:35.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:35.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:35.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:35.775][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:35.776][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:35.778][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:35.779][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:35.781][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:35.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:35.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:35.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:35.787][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:35.788][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:35.790][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:35.791][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:35.793][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:35.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:35.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:35.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:35.799][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:35.800][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:35.802][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:35.803][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:35.805][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:35.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:35.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:35.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:35.811][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:35.813][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:35.814][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:35.815][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:35.817][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:35.819][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:35.820][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:35.821][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:35.823][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:35.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:35.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:35.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:35.829][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:35.831][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:35.832][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:35.834][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:35.836][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:35.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:35.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:35.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:35.842][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:35.843][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:35.844][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:35.846][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:35.848][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:35.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:35.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:35.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:35.851][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:35.852][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:35.853][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:35.854][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:35.855][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:35.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:35.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:35.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:35.859][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:35.860][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:35.861][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:35.862][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:35.863][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:35.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:35.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:35.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:35.867][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:35.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:35.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:35.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:35.870][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:35.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:35.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:35.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:35.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:35.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:35.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:35.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:35.877][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:35.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:35.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:35.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:35.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:35.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:35.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:35.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:35.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:35.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:35.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:35.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:35.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:35.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:35.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:35.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:35.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:35.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:35.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:35.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:35.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:35.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:35.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:35.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:35.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:35.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:35.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:35.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:35.903][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-07-22 21:21:35.904][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:35.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:35.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:35.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:35.908][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:35.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:35.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:35.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:35.911][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:35.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:35.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:35.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:35.915][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:35.916][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:35.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:35.929][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:35.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:35.931][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:35.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:35.933][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-07-22 21:21:35.933][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-22 21:21:35.935][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-07-22 21:21:35.936][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-22 21:21:35.937][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-22 21:21:35.938][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-22 21:21:35.939][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-22 21:21:35.940][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-22 21:21:35.941][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-22 21:21:35.944][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:35.944][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:35.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:35.949][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:35.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:35.951][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:35.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:35.953][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-07-22 21:21:35.956][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:21:35.957][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:21:35.958][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-07-22 21:21:36.348][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-07-22 21:21:36.770][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:21:36.772][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-07-22 21:21:36.775][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-07-22 21:21:36.778][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-07-22 21:21:36.779][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-22 21:21:36.780][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-22 21:21:36.782][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-22 21:21:36.783][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:36.784][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:36.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:36.789][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:36.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:36.791][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:36.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:36.794][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:36.796][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:36.796][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:36.797][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:36.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:36.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:36.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:36.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:36.803][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:36.804][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:36.805][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:36.806][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:36.807][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:36.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:36.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:36.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:36.811][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:36.812][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:36.813][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:36.814][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:36.815][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:36.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:36.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:36.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:36.819][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:36.820][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:36.821][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:36.822][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:36.823][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:36.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:36.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:36.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:36.827][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:36.828][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:36.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:36.830][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:36.831][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:36.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:36.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:36.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:36.835][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:36.836][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:36.837][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:36.837][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:36.839][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:36.840][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:36.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:36.842][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:36.843][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:36.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:36.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:36.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:36.847][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:36.848][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:36.849][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:36.850][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:36.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:36.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:36.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:36.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:36.855][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:36.855][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:36.856][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:36.857][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:36.859][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:36.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:36.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:36.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:36.862][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:36.863][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:36.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:36.865][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:36.866][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:36.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:36.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:36.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:36.870][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:36.871][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:36.872][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:36.873][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:36.874][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:36.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:36.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:36.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:36.878][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:36.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:36.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:36.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:36.882][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:36.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:36.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:36.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:36.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:36.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:36.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:36.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:36.889][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:36.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:36.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:36.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:36.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:36.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:36.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:36.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:36.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:36.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:36.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:36.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:36.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:36.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:36.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:36.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:36.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:36.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:36.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:36.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:36.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:36.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:36.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:36.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:36.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:36.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:36.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:36.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:36.923][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-07-22 21:21:36.924][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:36.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:36.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:36.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:36.928][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:36.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:36.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:36.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:36.931][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:36.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:36.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:36.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:36.935][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:36.936][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:36.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:36.941][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:36.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:36.943][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:36.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:36.945][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-07-22 21:21:36.945][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-22 21:21:36.947][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-07-22 21:21:36.948][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-22 21:21:36.949][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-22 21:21:36.950][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-22 21:21:36.951][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-22 21:21:36.952][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-22 21:21:36.953][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-22 21:21:36.955][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:36.956][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:36.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:36.961][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:36.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:36.963][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:36.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:36.965][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-07-22 21:21:36.968][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:21:36.969][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:21:36.970][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-07-22 21:21:37.359][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-07-22 21:21:37.753][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:21:37.755][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-07-22 21:21:37.759][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-07-22 21:21:37.761][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-07-22 21:21:37.762][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-22 21:21:37.764][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-22 21:21:37.765][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-22 21:21:37.767][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:37.767][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:37.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:37.773][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:37.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:37.775][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:37.776][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[2024-07-22 21:21:37.778][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:37.779][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:37.780][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:37.781][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:37.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:37.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:37.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:37.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:37.787][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:37.788][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:37.789][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:37.790][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:37.791][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:37.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:37.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:37.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:37.795][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:37.796][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:37.797][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:37.798][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:37.799][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:37.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:37.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:37.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:37.803][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:37.804][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:37.805][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:37.806][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:37.807][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:37.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:37.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:37.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:37.811][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:37.812][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:37.813][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:37.814][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:37.815][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:37.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:37.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:37.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:37.819][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:37.820][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:37.821][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:37.822][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:37.823][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:37.824][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:37.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:37.826][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:37.827][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:37.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:37.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:37.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:37.831][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:37.832][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:37.833][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:37.834][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:37.835][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:37.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:37.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:37.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:37.838][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:37.839][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:37.840][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:37.841][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:37.843][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:37.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:37.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:37.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:37.846][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:37.847][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:37.848][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:37.849][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:37.850][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:37.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:37.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:37.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:37.863][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:37.864][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:37.865][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:37.865][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:37.867][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:37.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:37.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:37.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:37.871][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:37.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:37.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:37.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:37.874][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:37.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:37.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:37.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:37.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:37.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:37.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:37.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:37.882][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:37.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:37.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:37.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:37.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:37.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:37.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:37.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:37.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:37.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:37.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:37.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:37.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:37.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:37.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:37.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:37.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:37.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:37.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:37.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:37.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:37.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:37.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:37.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:37.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:37.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:37.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:37.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:37.908][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-07-22 21:21:37.909][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:37.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:37.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:37.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:37.912][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:37.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:37.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:37.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:37.916][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:37.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:37.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:37.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:37.920][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:37.920][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:37.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:37.925][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:37.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:37.927][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:37.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:37.929][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-07-22 21:21:37.930][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-22 21:21:37.931][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-07-22 21:21:37.933][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-22 21:21:37.934][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-22 21:21:37.935][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-22 21:21:37.936][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-22 21:21:37.937][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-22 21:21:37.937][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-22 21:21:37.940][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:37.941][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:37.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:37.946][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:37.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:37.947][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:37.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:37.949][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.INFO [2024-07-22 21:21:37.952][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.DEBUG[2024-07-22 21:21:37.953][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:21:37.954][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:21:37.955][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-07-22 21:21:38.342][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-07-22 21:21:38.774][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:21:38.777][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-07-22 21:21:38.783][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-07-22 21:21:38.787][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-07-22 21:21:38.790][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-22 21:21:38.792][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-22 21:21:38.794][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-22 21:21:38.797][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:38.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:38.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:38.807][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:38.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:38.811][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:38.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:38.816][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:38.818][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:38.819][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:38.821][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:38.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:38.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:38.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:38.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:38.829][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:38.830][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:38.831][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:38.833][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:38.834][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:38.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:38.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:38.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:38.839][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:38.840][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:38.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:38.842][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:38.844][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:38.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:38.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:38.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:38.848][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:38.849][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:38.850][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:38.851][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:38.853][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:38.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:38.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:38.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:38.856][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:38.857][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:38.858][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:38.859][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:38.860][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:38.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:38.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:38.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:38.864][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:38.865][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:38.866][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:38.900][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:38.908][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:38.909][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:38.910][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:38.911][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:38.913][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:38.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:38.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:38.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:38.917][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:38.918][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:38.919][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:38.920][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:38.921][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:38.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:38.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:38.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:38.925][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:38.926][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:38.927][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:38.928][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:38.930][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:38.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:38.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:38.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:38.934][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:38.935][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:38.936][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:38.937][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:38.938][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:38.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:38.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:38.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:38.943][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:38.944][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:38.945][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:38.946][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:38.947][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:38.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:38.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:38.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:38.951][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:38.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:38.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:38.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:38.954][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:38.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:38.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:38.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:38.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:38.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:38.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:38.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:38.962][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:38.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:38.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:38.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:38.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:38.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:38.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:38.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:38.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:38.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:38.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:38.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:38.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:38.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:38.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:38.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:38.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:38.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:38.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:38.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:38.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:38.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:38.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:38.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:38.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:38.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:38.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:38.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:38.987][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-07-22 21:21:38.988][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:38.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:38.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:38.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:38.992][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:38.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:38.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:38.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:38.995][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:38.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:38.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:38.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:38.999][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:39.000][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:39.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:39.005][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:39.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:39.006][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:39.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:39.008][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-07-22 21:21:39.009][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-22 21:21:39.011][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-07-22 21:21:39.012][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-22 21:21:39.013][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-22 21:21:39.014][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-22 21:21:39.015][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-22 21:21:39.016][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-22 21:21:39.017][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-22 21:21:39.019][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:39.020][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:39.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:39.025][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:39.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:39.027][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:39.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:39.029][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-07-22 21:21:39.031][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:21:39.032][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:21:39.033][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-07-22 21:21:39.418][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-07-22 21:21:39.851][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:21:39.854][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-07-22 21:21:39.867][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-07-22 21:21:39.872][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-07-22 21:21:39.874][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-22 21:21:39.877][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-22 21:21:39.879][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-22 21:21:39.882][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:39.883][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:39.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:39.894][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:39.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:39.897][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:39.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:39.904][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:39.906][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:39.908][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:39.909][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:39.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:39.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:39.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:39.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:39.917][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:39.919][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:39.920][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:39.922][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:39.924][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:39.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:39.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:39.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:39.957][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:39.958][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:39.960][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:39.961][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:39.963][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:39.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:39.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:39.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:39.970][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:39.972][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:39.973][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:39.974][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:39.975][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:39.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:39.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:39.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:39.979][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:39.980][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:39.981][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:39.982][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:39.983][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:39.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:39.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:39.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:39.987][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:39.988][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:39.989][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:39.990][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:39.992][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:39.993][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:39.993][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:39.994][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:39.996][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:39.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:39.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:39.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.000][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:40.001][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:40.002][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.003][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.004][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:40.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:40.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.008][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:40.009][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:40.010][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.011][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.012][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:40.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:40.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.016][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:40.017][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:40.018][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.019][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.020][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:40.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:40.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.024][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:40.025][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:40.026][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.027][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.029][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:40.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:40.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.033][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:40.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:40.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.037][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:40.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:40.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:40.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:40.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.044][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:40.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:40.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:40.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:40.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:40.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:40.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.056][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:40.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:40.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:40.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:40.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:40.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:40.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:40.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:40.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:40.072][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-07-22 21:21:40.073][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:40.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:40.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.077][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:40.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:40.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.081][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:40.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:40.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:40.085][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:40.086][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:40.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:40.091][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:40.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:40.093][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:40.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:40.095][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-07-22 21:21:40.096][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-22 21:21:40.097][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-07-22 21:21:40.098][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-22 21:21:40.099][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-22 21:21:40.100][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-22 21:21:40.101][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-22 21:21:40.102][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-22 21:21:40.103][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-22 21:21:40.106][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:40.106][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:40.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:40.111][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:40.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:40.113][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:40.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:40.115][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-07-22 21:21:40.118][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:21:40.118][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:21:40.120][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-07-22 21:21:40.512][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-07-22 21:21:40.902][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2024-07-22 21:21:40.903][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-07-22 21:21:40.905][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-07-22 21:21:40.908][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-07-22 21:21:40.919][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-07-22 21:21:40.920][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-22 21:21:40.922][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-22 21:21:40.923][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-22 21:21:40.924][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:40.925][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:40.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:40.930][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:40.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:40.932][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:40.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:40.935][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:40.936][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:40.937][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.938][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:40.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:40.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.943][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:40.944][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:40.945][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.946][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.947][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:40.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:40.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.951][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:40.952][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:40.952][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.953][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.954][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:40.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:40.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.958][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:40.959][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:40.960][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.961][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.962][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:40.963][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:40.964][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.965][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.966][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:40.967][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:40.968][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.969][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.970][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:40.971][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:40.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.973][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.974][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:40.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:40.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.978][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:40.979][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:40.980][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.980][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.982][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:40.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:40.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.985][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:40.986][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:40.987][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.988][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.990][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:40.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:40.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.993][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:40.994][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:40.995][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:40.996][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:40.997][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:40.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:40.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:41.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:41.001][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:41.002][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:41.003][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:41.004][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:41.005][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:41.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:41.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:41.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:41.009][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:41.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:41.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:41.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:41.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:41.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:41.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:41.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:41.016][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:41.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:41.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:41.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:41.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:41.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:41.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:41.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:41.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:41.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:41.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:41.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:41.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:41.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:41.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:41.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:41.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:41.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:41.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:41.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:41.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:41.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:41.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:41.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:41.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:41.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:41.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:41.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:41.042][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-07-22 21:21:41.043][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:41.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:41.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:41.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:41.047][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:41.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:41.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:41.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:41.051][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:41.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:41.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:41.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:41.055][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:41.056][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:41.056][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:41.061][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:41.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:41.063][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:41.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:41.064][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-07-22 21:21:41.065][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-22 21:21:41.067][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-07-22 21:21:41.068][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-22 21:21:41.069][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-22 21:21:41.070][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-22 21:21:41.071][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-22 21:21:41.072][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-22 21:21:41.073][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-22 21:21:41.076][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:41.077][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:41.077][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:41.088][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:41.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:41.090][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:41.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:41.092][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-07-22 21:21:41.095][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:21:41.096][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:21:41.098][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-07-22 21:21:41.485][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2024-07-22 21:21:41.918][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:21:41.922][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-07-22 21:21:41.929][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-07-22 21:21:41.935][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-07-22 21:21:41.938][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-22 21:21:41.940][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-22 21:21:41.943][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-22 21:21:41.946][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:41.948][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:41.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:41.959][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:41.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:41.963][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:41.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:41.969][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:41.971][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:41.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:41.974][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:41.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:41.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:41.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:41.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:41.982][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:41.983][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:41.984][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:41.986][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:41.987][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:41.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:41.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:41.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:41.992][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:41.993][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:41.995][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:41.996][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:41.997][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:41.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:41.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:42.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:42.002][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:42.003][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:42.004][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:42.005][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:42.006][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:42.007][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:42.008][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:42.009][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:42.010][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:42.011][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:42.012][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:42.013][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:42.014][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:42.015][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:42.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:42.017][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:42.018][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:42.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:42.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:42.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:42.022][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:42.023][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:42.023][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:42.024][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:42.025][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:42.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:42.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:42.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:42.029][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:42.030][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:42.031][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:42.032][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:42.033][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:42.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:42.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:42.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:42.037][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:42.038][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:42.039][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:42.040][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:42.041][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:42.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:42.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:42.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:42.044][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:42.045][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:42.046][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:42.047][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:42.048][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:42.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:42.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:42.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:42.052][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:42.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:42.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:42.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:42.056][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:42.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:42.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:42.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:42.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:42.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:42.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:42.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:42.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:42.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:42.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:42.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:42.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:42.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:42.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:42.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:42.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:42.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:42.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:42.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:42.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:42.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:42.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:42.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:42.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:42.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:42.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:42.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:42.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:42.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:42.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:42.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:42.085][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-07-22 21:21:42.086][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:42.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:42.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:42.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:42.089][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:42.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:42.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:42.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:42.093][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:42.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:42.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:42.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:42.097][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:42.097][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:42.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:42.102][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:42.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:42.104][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:42.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:42.114][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-07-22 21:21:42.115][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-22 21:21:42.117][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-07-22 21:21:42.118][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-22 21:21:42.119][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-22 21:21:42.120][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-22 21:21:42.121][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-22 21:21:42.122][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-22 21:21:42.123][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-22 21:21:42.125][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:42.126][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:42.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:42.131][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:42.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:42.134][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:42.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:42.136][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-07-22 21:21:42.139][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:21:42.140][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:21:42.141][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-07-22 21:21:42.527][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2024-07-22 21:21:42.965][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:21:42.970][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-07-22 21:21:42.977][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-07-22 21:21:42.982][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-07-22 21:21:42.985][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-22 21:21:42.988][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-22 21:21:42.990][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-22 21:21:42.994][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:42.996][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:42.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:43.007][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:43.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:43.010][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:43.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:43.016][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:43.018][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:43.019][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:43.021][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:43.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:43.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:43.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:43.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:43.028][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:43.030][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:43.031][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:43.032][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:43.034][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:43.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:43.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:43.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:43.039][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:43.040][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:43.041][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:43.042][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:43.044][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:43.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:43.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:43.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:43.048][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:43.050][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:43.051][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:43.052][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:43.053][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:43.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:43.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:43.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:43.057][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:43.058][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:43.059][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:43.060][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:43.061][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:43.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:43.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:43.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:43.065][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:43.066][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:43.066][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:43.067][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:43.069][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:43.070][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:43.070][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:43.071][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:43.072][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:43.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:43.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:43.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:43.076][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:43.077][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:43.078][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:43.079][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:43.080][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:43.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:43.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:43.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:43.084][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:43.085][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:43.086][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:43.086][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:43.088][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:43.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:43.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:43.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:43.092][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:43.092][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:43.093][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:43.094][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:43.095][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:43.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:43.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:43.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:43.099][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:43.100][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:43.101][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:43.102][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:43.103][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:43.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:43.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:43.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:43.107][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:43.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:43.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:43.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:43.111][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:43.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:43.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:43.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:43.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:43.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:43.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:43.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:43.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:43.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:43.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:43.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:43.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:43.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:43.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:43.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:43.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:43.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:43.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:43.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:43.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:43.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:43.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:43.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:43.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:43.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:43.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:43.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:43.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:43.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:43.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:43.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:43.152][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:43.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:43.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:43.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:43.156][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-07-22 21:21:43.157][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:43.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:43.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:43.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:43.161][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:43.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:43.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:43.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:43.166][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:43.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:43.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:43.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:43.170][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:43.171][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:43.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:43.177][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:43.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:43.179][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:43.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:43.181][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-07-22 21:21:43.182][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-22 21:21:43.183][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-07-22 21:21:43.185][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-22 21:21:43.186][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-22 21:21:43.187][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-22 21:21:43.188][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-22 21:21:43.189][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-22 21:21:43.190][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-22 21:21:43.192][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:43.193][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:43.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:43.199][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:43.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:43.201][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:43.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:43.203][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-07-22 21:21:43.206][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:21:43.207][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:21:43.208][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-07-22 21:21:43.608][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-07-22 21:21:43.996][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:21:44.000][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-07-22 21:21:44.007][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-07-22 21:21:44.012][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-07-22 21:21:44.015][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-22 21:21:44.018][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-22 21:21:44.020][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-22 21:21:44.024][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:44.026][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:44.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:44.037][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:44.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:44.040][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:44.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:44.046][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:44.048][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:44.049][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:44.051][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:44.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:44.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:44.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:44.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:44.059][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:44.060][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:44.062][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:44.063][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:44.065][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:44.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:44.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:44.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:44.070][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:44.071][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:44.072][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:44.073][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:44.075][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:44.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:44.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:44.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:44.079][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:44.080][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:44.081][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:44.082][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:44.083][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:44.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:44.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:44.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:44.087][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:44.088][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:44.089][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:44.090][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:44.091][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:44.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:44.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:44.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:44.095][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:44.096][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:44.097][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:44.098][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:44.099][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:44.100][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:44.101][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:44.101][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:44.103][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:44.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:44.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:44.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:44.106][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:44.107][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:44.108][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:44.109][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:44.110][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:44.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:44.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:44.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:44.114][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:44.115][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:44.116][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:44.116][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:44.118][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:44.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:44.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:44.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:44.121][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:44.122][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:44.123][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:44.124][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:44.125][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:44.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:44.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:44.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:44.129][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:44.130][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:44.131][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:44.132][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:44.133][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:44.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:44.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:44.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:44.137][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:44.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:44.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:44.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:44.149][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:44.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:44.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:44.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:44.152][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:44.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:44.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:44.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:44.156][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:44.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:44.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:44.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:44.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:44.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:44.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:44.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:44.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:44.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:44.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:44.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:44.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:44.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:44.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:44.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:44.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:44.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:44.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:44.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:44.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:44.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:44.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:44.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:44.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:44.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:44.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:44.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:44.182][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-07-22 21:21:44.183][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:44.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:44.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:44.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:44.186][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:44.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:44.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:44.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:44.190][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:44.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:44.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:44.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:44.193][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:44.194][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:44.195][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:44.199][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:44.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:44.201][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:44.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:44.203][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-07-22 21:21:44.204][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-22 21:21:44.205][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-07-22 21:21:44.206][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-22 21:21:44.207][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-22 21:21:44.208][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-22 21:21:44.209][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-22 21:21:44.210][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-22 21:21:44.211][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-22 21:21:44.214][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:44.214][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:44.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:44.219][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:44.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:44.221][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:44.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:44.223][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-07-22 21:21:44.225][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:21:44.226][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:21:44.228][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-07-22 21:21:44.613][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-07-22 21:21:45.047][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:21:45.050][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-07-22 21:21:45.054][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-07-22 21:21:45.058][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-07-22 21:21:45.060][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-22 21:21:45.062][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-22 21:21:45.063][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-22 21:21:45.066][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:45.067][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:45.068][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:45.074][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:45.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:45.077][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:45.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:45.081][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:45.083][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:45.084][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:45.085][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:45.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:45.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:45.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:45.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:45.092][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:45.094][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:45.095][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:45.096][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:45.098][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:45.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:45.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:45.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:45.104][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:45.105][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:45.107][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:45.108][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:45.110][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:45.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:45.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:45.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:45.115][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:45.117][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:45.118][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:45.119][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:45.121][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:45.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:45.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:45.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:45.127][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:45.128][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:45.129][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:45.131][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:45.132][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:45.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:45.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:45.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:45.138][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:45.139][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:45.140][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:45.142][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:45.143][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:45.145][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:45.146][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:45.147][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:45.149][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:45.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:45.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:45.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:45.155][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:45.156][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:45.169][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:45.171][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:45.172][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:45.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:45.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:45.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:45.176][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:45.177][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:45.177][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:45.178][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:45.180][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:45.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:45.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:45.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:45.183][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:45.184][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:45.185][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:45.186][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:45.187][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:45.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:45.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:45.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:45.191][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:45.192][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:45.193][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:45.194][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:45.195][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:45.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:45.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:45.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:45.199][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:45.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:45.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:45.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:45.202][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:45.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:45.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:45.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:45.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:45.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:45.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:45.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:45.209][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:45.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:45.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:45.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:45.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:45.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:45.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:45.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:45.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:45.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:45.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:45.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:45.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:45.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:45.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:45.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:45.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:45.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:45.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:45.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:45.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:45.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:45.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:45.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:45.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:45.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:45.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:45.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:45.235][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-07-22 21:21:45.236][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:45.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:45.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:45.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:45.239][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:45.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:45.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:45.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:45.243][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:45.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:45.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:45.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:45.247][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:45.247][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:45.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:45.252][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:45.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:45.254][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:45.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:45.256][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-07-22 21:21:45.257][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-22 21:21:45.258][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-07-22 21:21:45.259][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-22 21:21:45.260][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-22 21:21:45.261][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-22 21:21:45.262][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-22 21:21:45.263][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-22 21:21:45.264][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-22 21:21:45.267][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:45.267][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:45.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:45.273][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:45.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:45.274][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:45.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:45.276][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-07-22 21:21:45.279][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:21:45.280][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:21:45.281][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-07-22 21:21:45.669][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-07-22 21:21:46.059][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:21:46.061][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-07-22 21:21:46.065][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-07-22 21:21:46.067][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-07-22 21:21:46.069][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-22 21:21:46.070][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-22 21:21:46.071][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-22 21:21:46.073][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:46.074][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:46.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:46.079][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:46.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:46.081][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:46.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:46.084][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:46.085][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:46.086][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:46.087][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:46.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:46.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:46.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:46.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:46.092][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:46.093][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:46.094][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:46.095][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:46.096][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:46.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:46.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:46.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:46.100][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:46.101][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:46.102][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:46.103][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:46.104][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:46.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:46.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:46.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:46.117][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:46.118][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:46.119][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:46.120][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:46.121][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:46.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:46.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:46.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:46.125][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:46.126][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:46.126][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:46.127][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:46.128][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:46.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:46.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:46.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:46.132][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:46.133][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:46.134][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:46.135][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:46.136][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:46.137][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:46.138][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:46.139][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:46.140][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:46.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:46.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:46.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:46.144][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:46.145][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:46.146][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:46.147][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:46.148][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:46.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:46.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:46.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:46.152][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:46.153][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:46.154][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:46.154][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:46.156][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:46.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:46.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:46.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:46.160][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:46.161][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:46.161][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:46.162][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:46.163][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:46.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:46.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:46.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:46.167][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:46.168][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:46.169][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:46.170][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:46.171][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:46.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:46.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:46.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:46.175][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:46.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:46.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:46.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:46.179][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:46.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:46.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:46.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:46.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:46.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:46.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:46.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:46.186][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:46.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:46.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:46.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:46.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:46.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:46.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:46.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:46.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:46.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:46.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:46.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:46.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:46.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:46.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:46.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:46.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:46.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:46.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:46.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:46.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:46.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:46.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:46.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:46.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:46.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:46.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:46.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:46.212][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-07-22 21:21:46.213][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:46.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:46.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:46.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:46.217][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:46.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:46.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:46.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:46.221][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:46.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:46.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:46.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:46.224][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:46.225][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:46.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:46.230][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:46.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:46.232][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:46.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:46.234][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-07-22 21:21:46.235][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-22 21:21:46.237][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-07-22 21:21:46.238][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-22 21:21:46.239][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-22 21:21:46.240][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-22 21:21:46.241][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-22 21:21:46.242][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-22 21:21:46.243][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-22 21:21:46.246][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:46.246][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:46.247][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:46.252][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:46.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:46.253][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:46.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:46.255][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-07-22 21:21:46.258][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:21:46.259][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:21:46.260][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-07-22 21:21:46.648][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-07-22 21:21:47.074][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:21:47.077][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-07-22 21:21:47.080][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-07-22 21:21:47.082][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-07-22 21:21:47.084][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-22 21:21:47.085][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-22 21:21:47.086][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-22 21:21:47.088][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:47.089][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:47.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:47.105][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:47.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:47.107][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:47.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:47.111][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:47.112][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:47.113][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:47.114][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:47.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:47.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:47.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:47.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:47.119][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:47.120][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:47.122][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:47.122][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:47.124][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:47.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:47.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:47.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:47.128][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:47.129][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:47.130][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:47.131][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:47.132][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:47.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:47.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:47.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:47.136][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:47.137][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:47.138][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:47.139][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:47.140][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:47.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:47.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:47.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:47.144][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:47.145][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:47.146][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:47.147][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:47.148][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:47.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:47.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:47.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:47.152][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:47.153][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:47.154][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:47.154][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:47.156][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:47.157][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:47.158][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:47.158][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:47.160][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:47.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:47.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:47.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:47.164][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:47.164][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:47.165][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:47.166][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:47.167][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:47.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:47.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:47.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:47.171][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:47.172][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:47.173][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:47.174][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:47.175][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:47.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:47.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:47.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:47.179][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:47.180][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:47.181][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:47.182][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:47.183][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:47.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:47.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:47.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:47.187][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:47.188][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:47.189][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:47.190][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:47.191][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:47.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:47.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:47.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:47.195][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:47.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:47.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:47.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:47.198][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:47.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:47.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:47.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:47.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:47.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:47.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:47.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:47.206][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:47.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:47.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:47.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:47.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:47.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:47.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:47.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:47.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:47.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:47.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:47.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:47.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:47.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:47.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:47.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:47.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:47.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:47.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:47.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:47.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:47.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:47.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:47.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:47.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:47.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:47.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:47.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:47.232][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-07-22 21:21:47.233][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:47.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:47.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:47.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:47.237][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:47.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:47.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:47.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:47.240][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:47.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:47.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:47.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:47.244][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:47.245][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:47.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:47.250][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:47.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:47.251][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:47.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:47.253][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-07-22 21:21:47.254][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-22 21:21:47.256][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-07-22 21:21:47.257][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-22 21:21:47.258][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-22 21:21:47.259][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-22 21:21:47.260][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-22 21:21:47.261][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-22 21:21:47.262][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-22 21:21:47.264][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:47.265][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:47.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:47.275][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:47.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:47.277][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:47.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:47.279][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-07-22 21:21:47.281][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:21:47.282][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:21:47.284][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-07-22 21:21:47.671][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-07-22 21:21:48.094][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:21:48.098][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-07-22 21:21:48.113][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-07-22 21:21:48.122][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-07-22 21:21:48.126][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-22 21:21:48.129][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-22 21:21:48.132][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-22 21:21:48.137][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:48.139][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:48.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:48.152][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:48.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:48.156][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:48.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:48.161][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:48.163][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:48.164][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:48.165][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:48.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:48.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:48.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:48.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:48.173][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:48.174][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:48.175][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:48.177][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:48.178][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:48.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:48.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:48.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:48.183][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:48.184][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:48.185][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:48.186][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:48.188][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:48.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:48.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:48.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:48.192][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:48.193][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:48.194][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:48.195][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:48.197][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:48.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:48.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:48.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:48.201][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:48.202][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:48.203][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:48.204][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:48.206][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:48.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:48.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:48.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:48.210][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:48.211][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:48.212][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:48.213][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:48.215][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:48.216][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:48.217][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:48.218][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:48.220][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:48.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:48.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:48.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:48.224][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:48.225][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:48.226][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:48.227][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:48.228][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:48.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:48.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:48.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:48.233][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:48.234][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:48.235][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:48.236][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:48.238][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:48.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:48.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:48.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:48.242][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:48.243][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:48.244][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:48.246][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:48.247][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:48.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:48.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:48.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:48.252][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:48.254][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:48.255][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:48.256][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:48.257][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:48.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:48.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:48.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:48.263][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:48.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:48.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:48.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:48.267][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:48.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:48.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:48.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:48.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:48.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:48.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:48.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:48.276][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:48.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:48.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:48.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:48.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:48.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:48.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:48.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:48.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:48.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:48.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:48.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:48.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:48.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:48.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:48.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:48.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:48.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:48.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:48.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:48.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:48.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:48.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:48.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:48.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:48.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:48.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:48.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:48.304][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-07-22 21:21:48.306][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:48.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:48.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:48.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:48.328][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:48.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:48.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:48.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:48.333][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:48.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:48.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:48.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:48.337][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:48.337][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:48.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:48.343][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:48.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:48.345][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:48.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:48.347][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-07-22 21:21:48.348][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-22 21:21:48.350][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-07-22 21:21:48.351][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-22 21:21:48.352][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-22 21:21:48.353][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-22 21:21:48.354][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-22 21:21:48.355][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-22 21:21:48.356][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-22 21:21:48.358][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:48.359][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:48.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:48.365][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:48.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:48.366][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:48.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:48.368][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2024-07-22 21:21:48.371][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:21:48.372][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:21:48.373][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-07-22 21:21:48.760][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-07-22 21:21:49.174][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:21:49.179][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-07-22 21:21:49.186][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-07-22 21:21:49.191][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-07-22 21:21:49.194][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-22 21:21:49.197][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-22 21:21:49.200][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-22 21:21:49.203][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:49.205][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:49.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:49.216][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:49.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:49.219][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:49.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:49.225][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:49.227][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:49.228][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:49.230][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:49.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:49.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:49.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:49.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:49.238][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:49.239][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:49.240][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:49.241][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:49.243][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:49.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:49.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:49.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:49.248][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:49.249][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:49.250][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:49.252][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:49.253][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:49.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:49.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:49.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:49.257][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:49.259][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:49.260][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:49.261][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:49.262][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:49.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:49.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:49.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:49.266][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:49.267][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:49.268][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:49.269][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:49.270][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:49.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:49.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:49.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:49.274][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:49.275][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:49.276][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:49.276][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:49.278][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:49.279][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:49.279][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:49.280][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:49.281][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:49.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:49.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:49.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:49.285][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:49.286][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:49.287][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:49.288][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:49.289][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:49.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:49.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:49.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:49.293][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:49.294][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:49.295][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:49.296][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:49.297][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:49.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:49.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:49.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:49.301][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:49.302][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:49.303][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:49.303][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:49.305][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:49.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:49.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:49.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:49.308][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:49.309][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:49.310][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:49.311][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:49.312][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:49.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:49.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:49.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:49.316][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:49.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:49.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:49.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:49.319][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:49.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:49.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:49.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:49.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:49.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:49.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:49.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:49.336][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:49.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:49.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:49.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:49.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:49.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:49.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:49.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:49.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:49.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:49.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:49.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:49.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:49.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:49.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:49.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:49.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:49.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:49.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:49.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:49.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:49.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:49.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:49.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:49.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:49.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:49.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:49.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:49.363][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-07-22 21:21:49.364][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:49.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:49.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:49.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:49.367][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:49.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:49.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:49.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:49.371][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:49.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:49.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:49.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:49.391][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-22 21:21:49.394][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:21:49.395][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:21:49.397][private$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[2024-07-22 21:21:49.922][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[2024-07-22 21:21:50.476][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:21:50.479][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-07-22 21:21:50.485][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-07-22 21:21:50.491][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:50.493][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:50.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:50.502][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:50.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:50.505][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:50.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:50.508][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.515][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.522][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:50.528][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:50.529][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:50.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:50.536][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:50.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:50.538][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:50.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:50.541][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.545][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.549][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.554][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.557][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:50.561][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:50.562][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:50.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:50.567][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:50.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:50.569][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:50.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:50.571][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.574][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.578][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.582][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.585][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:50.589][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:50.590][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:50.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:50.595][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:50.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:50.596][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:50.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:50.598][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.610][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.614][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.618][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.622][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:50.625][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:50.626][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:50.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:50.631][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:50.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:50.633][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:50.634][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[2024-07-22 21:21:50.635][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.639][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.642][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:50.646][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:50.647][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:50.648][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:50.652][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:50.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:50.654][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:50.654][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.TRACE[2024-07-22 21:21:50.655][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.659][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.663][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:50.667][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:50.668][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:50.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:50.673][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:50.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:50.675][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:50.675][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.TRACE[2024-07-22 21:21:50.677][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.680][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.684][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:50.688][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:50.688][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:50.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:50.693][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:50.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:50.695][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:50.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:50.697][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.701][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.704][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:50.708][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:50.709][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:50.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:50.714][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:50.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:50.716][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:50.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:50.718][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.721][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.725][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:50.729][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:50.730][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:50.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:50.735][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:50.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:50.736][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:50.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:50.738][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.742][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.746][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:50.749][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:50.750][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:50.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:50.755][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:50.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:50.757][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:50.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:50.759][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.762][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.766][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:50.775][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:50.776][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:50.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:50.781][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:50.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:50.783][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:50.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:50.784][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.788][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.792][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:50.796][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:50.796][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:50.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:50.801][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:50.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:50.803][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:50.804][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.TRACE[2024-07-22 21:21:50.805][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.809][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.812][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:50.816][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:50.817][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:50.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:50.823][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:50.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:50.824][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:50.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:50.826][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.830][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.834][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:50.837][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:50.838][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:50.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:50.843][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:50.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:50.845][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:50.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:50.847][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.851][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.854][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:50.858][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:50.859][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:50.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:50.864][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:50.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:50.866][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:50.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:50.868][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.871][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.875][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:50.879][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:50.879][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:50.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:50.885][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:50.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:50.886][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:50.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:50.888][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.892][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.895][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:50.899][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:50.900][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:50.901][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:50.905][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:50.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:50.907][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:50.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:50.908][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.912][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.916][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:50.919][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:50.920][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:50.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:50.925][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:50.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:50.927][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:50.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:50.928][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.937][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.941][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:50.944][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:50.945][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:50.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:50.950][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:50.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:50.952][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:50.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:50.954][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.958][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.961][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:50.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.977][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:50.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:50.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.981][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:50.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:50.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.985][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:50.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:50.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.988][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:50.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:50.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:50.992][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:50.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:50.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:50.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:51.019][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[2024-07-22 21:21:51.022][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:21:51.023][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:21:51.025][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-22 21:21:51.411][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-22 21:21:51.823][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:21:51.827][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2024-07-22 21:21:51.834][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2024-07-22 21:21:51.840][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-22 21:21:51.846][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:21:51.847][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:21:51.851][private$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[2024-07-22 21:21:52.267][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[2024-07-22 21:21:52.702][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:21:52.705][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2024-07-22 21:21:52.712][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2024-07-22 21:21:52.717][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:52.718][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:52.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:52.727][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:52.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:52.730][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:52.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:52.734][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-07-22 21:21:52.736][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-22 21:21:52.738][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-07-22 21:21:52.740][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-22 21:21:52.742][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-22 21:21:52.744][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-22 21:21:52.746][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-22 21:21:52.748][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-22 21:21:52.749][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-22 21:21:52.753][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:52.754][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:52.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:52.761][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:52.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:52.764][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:52.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:52.766][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2024-07-22 21:21:52.769][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:21:52.771][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:21:52.772][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2024-07-22 21:21:53.173][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2024-07-22 21:21:53.586][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:21:53.590][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2024-07-22 21:21:53.597][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2024-07-22 21:21:53.601][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2024-07-22 21:21:53.604][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-22 21:21:53.607][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-22 21:21:53.609][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-22 21:21:53.612][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:53.614][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:53.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:53.624][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:53.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:53.628][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:53.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:53.633][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:53.635][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:53.636][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.638][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:53.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:53.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.645][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:53.647][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:53.648][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.649][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.651][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:53.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:53.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.656][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:53.657][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:53.658][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.659][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.661][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:53.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:53.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.665][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:53.666][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:53.667][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.668][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.670][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:53.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:53.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.674][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:53.675][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:53.676][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.676][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.678][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:53.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:53.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.681][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:53.682][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:53.683][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.684][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.685][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:53.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:53.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.689][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:53.690][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:53.691][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.692][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.693][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:53.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:53.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.697][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:53.697][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:53.698][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.699][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.700][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:53.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:53.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.704][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:53.705][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:53.706][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.707][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.708][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:53.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:53.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.712][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:53.713][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:53.714][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.715][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.716][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:53.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:53.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.720][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:53.721][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:53.721][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.722][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.723][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:53.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:53.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.727][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:53.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:53.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.731][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:53.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:53.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:53.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:53.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.738][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:53.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:53.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:53.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:53.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:53.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:53.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:53.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:53.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:53.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:53.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:53.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:53.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:53.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:53.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:53.764][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-07-22 21:21:53.766][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:53.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:53.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:53.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:53.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.773][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:53.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:53.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:53.785][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:53.786][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:53.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:53.791][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:53.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:53.793][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:53.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:53.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:53.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:53.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.799][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:53.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:53.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:53.803][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:53.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:53.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:53.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:53.806][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:53.807][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:53.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:53.812][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:53.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:53.814][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:53.815][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[2024-07-22 21:21:53.816][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-07-22 21:21:53.817][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-22 21:21:53.819][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-07-22 21:21:53.820][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-22 21:21:53.821][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-22 21:21:53.822][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-22 21:21:53.823][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-22 21:21:53.824][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-22 21:21:53.825][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-22 21:21:53.828][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:53.828][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:53.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:53.834][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:53.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:53.836][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:53.837][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[2024-07-22 21:21:53.838][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2024-07-22 21:21:53.841][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:21:53.842][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:21:53.843][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2024-07-22 21:21:54.228][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2024-07-22 21:21:54.654][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:21:54.657][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2024-07-22 21:21:54.663][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2024-07-22 21:21:54.667][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2024-07-22 21:21:54.670][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-22 21:21:54.672][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-22 21:21:54.674][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-22 21:21:54.677][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:54.678][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:54.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:54.687][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:54.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:54.690][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:54.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:54.695][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:54.697][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:54.699][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.700][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:54.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:54.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.708][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:54.710][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:54.711][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.712][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.714][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:21:54.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:21:54.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.719][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:54.720][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:54.721][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.722][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.724][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:21:54.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:21:54.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.728][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:54.729][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:54.730][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.731][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.732][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:21:54.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:21:54.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.736][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:54.737][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:54.738][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.739][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.740][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:21:54.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:21:54.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.744][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:54.745][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:21:54.746][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.747][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.749][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:54.750][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:54.751][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.752][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.753][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:21:54.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:54.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.757][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.758][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.759][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.759][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.761][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.764][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:54.765][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:54.766][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.767][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.769][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:21:54.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:21:54.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.772][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:54.773][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:54.774][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.775][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.776][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:21:54.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:21:54.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.780][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:54.781][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:54.782][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.782][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.784][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:21:54.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:21:54.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.796][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:54.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:54.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.799][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:54.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:54.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:54.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:54.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.807][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:54.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:54.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:54.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:54.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:54.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:54.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:54.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:54.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:54.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:54.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:54.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:54.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:21:54.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:21:54.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:54.832][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-07-22 21:21:54.833][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.837][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:54.860][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[2024-07-22 21:21:54.863][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-22 21:21:54.864][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-07-22 21:21:54.865][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-22 21:21:54.867][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-07-22 21:21:54.870][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:54.870][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:54.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:54.876][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:54.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:54.877][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:54.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:54.879][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.883][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.887][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:54.891][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:54.891][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:54.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:54.897][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:54.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:54.899][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:54.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:54.901][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.904][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.908][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.912][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.915][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:54.919][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:54.920][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:54.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:54.925][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:54.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:54.927][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:54.928][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.TRACE[2024-07-22 21:21:54.929][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.932][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.936][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.940][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.944][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:54.948][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:54.949][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:54.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:54.959][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:54.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:54.961][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:54.962][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.TRACE[2024-07-22 21:21:54.963][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.966][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.970][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.974][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.978][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:54.982][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:54.982][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:54.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:54.987][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:54.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:54.989][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:54.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:54.991][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.995][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:54.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:54.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:54.999][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.002][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.003][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.008][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.010][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:55.012][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.016][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.019][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.023][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.024][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.029][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.031][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:55.033][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.037][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.041][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.044][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.045][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.051][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.052][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:55.054][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.058][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.062][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.066][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.066][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.072][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.073][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.074][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[2024-07-22 21:21:55.075][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.079][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.083][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.086][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.087][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.092][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.094][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.095][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[2024-07-22 21:21:55.096][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.099][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.103][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.107][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.108][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.113][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.114][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:55.116][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.125][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.129][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.132][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.133][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.138][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.140][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.141][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.TRACE[2024-07-22 21:21:55.142][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.146][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.150][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.153][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.154][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.159][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.161][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.162][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[2024-07-22 21:21:55.163][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.166][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.170][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.174][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.175][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.180][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.181][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:55.183][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.187][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.191][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.194][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.195][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.200][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.202][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:55.204][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.207][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.211][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.215][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.216][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.221][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.223][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:55.224][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.228][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.232][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.235][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.236][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.241][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.243][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:55.245][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.249][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.253][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.256][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.257][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.262][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.264][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:55.266][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.269][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.273][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.276][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.277][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.293][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.295][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:55.297][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.300][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.304][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.308][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.309][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.314][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.316][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:55.318][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.322][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.325][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.345][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[2024-07-22 21:21:55.348][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-22 21:21:55.349][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-07-22 21:21:55.351][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-22 21:21:55.352][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-07-22 21:21:55.355][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.355][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.361][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.362][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.363][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[2024-07-22 21:21:55.364][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.368][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.372][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.375][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.376][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.381][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.383][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.384][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[2024-07-22 21:21:55.385][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.393][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.396][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.400][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.404][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.405][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.405][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.410][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.411][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:55.413][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.417][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.421][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.425][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.429][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.433][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.434][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.439][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.441][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:55.443][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.447][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.451][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.454][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.465][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.469][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.470][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.475][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.477][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:55.479][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.483][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.486][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.490][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.491][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.496][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.498][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.499][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[2024-07-22 21:21:55.500][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.504][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.508][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.511][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.512][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.517][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.519][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:55.521][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.525][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.528][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.532][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.533][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.538][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.540][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:55.542][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.546][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.549][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.553][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.559][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.561][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:55.563][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.567][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.571][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.574][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.575][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.580][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.582][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:55.584][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.588][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.592][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.595][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.596][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.602][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.603][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:55.605][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.609][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.613][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.616][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.617][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.618][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.622][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.624][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.625][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[2024-07-22 21:21:55.631][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.635][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.639][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.642][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.643][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.648][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.650][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:55.652][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.656][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.659][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.663][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.664][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.669][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.671][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.672][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.TRACE[2024-07-22 21:21:55.673][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.677][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.680][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.684][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.685][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.686][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.690][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.691][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.692][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[2024-07-22 21:21:55.693][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.697][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.701][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.704][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.705][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.710][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.712][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:55.714][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.717][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.721][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.725][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.725][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.730][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.732][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:55.734][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.738][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.741][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.745][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.751][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.753][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:55.754][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.758][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.762][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.766][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.766][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.771][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.773][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:55.775][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.779][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.782][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.786][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.787][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.797][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.799][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:55.801][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.805][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.809][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:55.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.825][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-07-22 21:21:55.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-07-22 21:21:55.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-22 21:21:55.835][biodb::testThat]
biodb.INFO [2024-07-22 21:21:55.836][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-07-22 21:21:55.837][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-22 21:21:55.838][biodb::testThat]
biodb.TRACE[2024-07-22 21:21:55.841][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-22 21:21:55.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-22 21:21:55.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.845][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:55.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:55.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.848][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:55.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:55.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.852][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:55.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:55.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:55.856][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:55.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:55.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:55.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:55.863][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:55.864][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:55.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:55.869][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:55.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:55.870][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:55.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:55.874][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[2024-07-22 21:21:55.877][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:21:55.878][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:21:55.880][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-22 21:21:56.267][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-22 21:21:56.673][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:21:56.675][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-07-22 21:21:56.679][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-07-22 21:21:56.681][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:56.682][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:56.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:56.687][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:56.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:56.689][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:56.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:56.691][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:56.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:56.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:56.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:56.695][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:56.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:56.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:56.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:56.699][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:56.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:56.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:56.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:56.704][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-22 21:21:56.707][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:21:56.708][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:21:56.709][private$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[2024-07-22 21:21:57.093][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[2024-07-22 21:21:57.493][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:21:57.500][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-07-22 21:21:57.508][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-07-22 21:21:57.514][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:57.516][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:57.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:57.528][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:57.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:57.532][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:57.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:57.536][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:57.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:57.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:57.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:57.542][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:57.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:57.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:57.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:57.548][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:57.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:57.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:57.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:57.554][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:57.555][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:57.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:57.562][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:57.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:57.564][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:57.581][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[2024-07-22 21:21:57.589][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:57.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:57.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:57.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:57.595][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:57.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:57.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:57.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:57.599][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:57.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:57.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:57.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:57.603][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-22 21:21:57.605][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:57.606][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:57.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:57.611][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:57.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:57.613][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:57.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:57.615][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:57.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:57.619][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:57.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:57.623][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:21:57.623][private$selectFields]
biodb.TRACE[2024-07-22 21:21:57.624][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-22 21:21:57.625][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-22 21:21:57.626][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:21:57.627][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.628][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.629][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:57.630][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:57.631][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.632][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.633][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:57.634][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:57.635][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:21:57.636][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:21:57.637][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.638][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.639][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:57.640][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:57.641][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-22 21:21:57.642][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:57.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:57.646][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:57.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:57.650][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:57.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:57.663][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-07-22 21:21:57.665][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:57.665][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:57.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:57.671][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:57.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:57.673][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:57.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:57.675][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:57.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:57.678][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:57.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:57.682][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:21:57.683][private$selectFields]
biodb.TRACE[2024-07-22 21:21:57.684][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-22 21:21:57.685][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-22 21:21:57.686][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:21:57.687][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.688][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.689][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:57.690][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:57.691][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.692][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.693][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:57.694][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:57.695][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:21:57.696][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:21:57.697][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.698][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.699][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:57.700][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:57.701][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-22 21:21:57.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:57.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:57.706][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:57.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:57.710][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:57.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:57.714][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-07-22 21:21:57.715][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:57.716][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:57.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:57.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:57.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:57.722][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:57.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:57.724][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:57.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:57.728][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:57.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:57.732][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:21:57.733][private$selectFields]
biodb.TRACE[2024-07-22 21:21:57.733][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-22 21:21:57.734][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-22 21:21:57.736][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:21:57.736][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.737][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.738][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:57.739][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:57.740][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.741][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.742][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:57.743][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:57.744][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:21:57.745][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:21:57.745][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.746][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.747][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:57.748][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:57.749][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-22 21:21:57.750][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:57.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:57.759][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:57.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:57.763][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:57.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:57.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:57.767][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-07-22 21:21:57.768][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-22 21:21:57.769][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-22 21:21:57.778][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:57.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:57.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:57.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:57.781][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:57.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:57.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:57.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:57.785][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:57.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:57.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:57.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:57.789][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:57.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:57.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:57.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:57.844][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:57.845][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:57.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:57.850][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:57.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:57.852][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:57.852][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[2024-07-22 21:21:57.855][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[2024-07-22 21:21:57.858][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:21:57.859][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:21:57.861][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-22 21:21:58.244][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-22 21:21:58.628][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:21:58.630][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-07-22 21:21:58.634][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-07-22 21:21:58.637][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-22 21:21:58.640][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:21:58.641][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:21:58.642][private$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[2024-07-22 21:21:59.031][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[2024-07-22 21:21:59.464][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:21:59.466][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-07-22 21:21:59.469][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-07-22 21:21:59.472][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:59.473][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:59.474][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:59.478][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:59.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:59.480][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:59.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:59.482][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:59.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:59.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.486][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:59.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:59.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.502][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:59.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:59.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:59.506][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:59.507][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:59.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:59.512][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:59.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:59.514][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:59.515][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[2024-07-22 21:21:59.516][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:59.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:59.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.520][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:59.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:59.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.523][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:59.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:59.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:59.527][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:59.528][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:59.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:59.533][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:59.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:59.535][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:59.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:59.537][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:59.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:59.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.540][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:59.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:59.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.544][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:59.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:21:59.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:59.571][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-22 21:21:59.596][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:59.597][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:59.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:59.603][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:59.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:59.605][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:59.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:59.607][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.611][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.615][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:21:59.616][private$selectFields]
biodb.TRACE[2024-07-22 21:21:59.617][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-22 21:21:59.618][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-22 21:21:59.619][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:21:59.620][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.621][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.622][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.623][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.624][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.625][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.626][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.627][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.628][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:21:59.629][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:21:59.630][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.631][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.632][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.633][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.634][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-22 21:21:59.635][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.639][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.643][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.647][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-07-22 21:21:59.648][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:59.649][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:59.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:59.660][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:59.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:59.662][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:59.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:59.676][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.680][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.704][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:21:59.705][private$selectFields]
biodb.TRACE[2024-07-22 21:21:59.706][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-22 21:21:59.707][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-22 21:21:59.708][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:21:59.709][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.710][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.711][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.712][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.713][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.714][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.715][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.715][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.716][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:21:59.727][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:21:59.728][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.729][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.730][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.730][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.731][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-22 21:21:59.732][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.736][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.740][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.744][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-07-22 21:21:59.745][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:59.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:59.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:59.751][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:59.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:59.752][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:59.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:59.754][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.758][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.762][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:21:59.763][private$selectFields]
biodb.TRACE[2024-07-22 21:21:59.764][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-22 21:21:59.764][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-22 21:21:59.765][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:21:59.766][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.767][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.768][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.769][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.770][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.771][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.772][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.773][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.774][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:21:59.775][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:21:59.775][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.776][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.777][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.778][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.779][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-22 21:21:59.780][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.784][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.788][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.792][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-07-22 21:21:59.792][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-22 21:21:59.793][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-22 21:21:59.802][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-07-22 21:21:59.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-07-22 21:21:59.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-22 21:21:59.814][biodb::testThat]
biodb.INFO [2024-07-22 21:21:59.815][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-07-22 21:21:59.816][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-22 21:21:59.817][biodb::testThat]
biodb.TRACE[2024-07-22 21:21:59.820][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-22 21:21:59.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-22 21:21:59.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.824][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:59.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:59.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.827][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:59.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:59.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.831][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:59.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:59.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.835][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:59.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:59.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:59.841][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:59.842][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:59.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:59.847][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:59.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:59.849][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:59.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:21:59.852][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[2024-07-22 21:21:59.856][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-22 21:21:59.857][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-07-22 21:21:59.858][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-22 21:21:59.859][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-07-22 21:21:59.861][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:59.862][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:59.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:59.867][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:59.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:59.869][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:59.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:59.871][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:59.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:59.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.875][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:59.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:59.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.878][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:59.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:59.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:59.883][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[2024-07-22 21:21:59.886][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-22 21:21:59.887][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-07-22 21:21:59.888][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-22 21:21:59.890][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-07-22 21:21:59.892][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:59.893][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:59.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:59.898][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:59.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:59.900][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:59.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:59.902][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:59.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:59.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.906][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:59.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:59.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.909][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:59.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:59.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:59.913][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:59.914][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:59.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:59.920][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:59.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:59.922][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:59.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:59.924][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:59.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:59.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.927][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:59.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:59.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.931][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:59.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:21:59.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:21:59.935][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-22 21:21:59.937][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:59.938][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:59.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:59.943][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:59.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:21:59.945][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:21:59.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:21:59.947][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.951][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.955][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:21:59.956][private$selectFields]
biodb.TRACE[2024-07-22 21:21:59.956][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-22 21:21:59.957][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-22 21:21:59.958][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:21:59.959][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.960][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.961][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.962][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.963][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.964][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.965][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.966][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.967][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:21:59.968][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:21:59.969][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.970][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.971][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.972][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.973][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-22 21:21:59.974][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.983][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.987][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:21:59.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:21:59.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:21:59.991][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-07-22 21:21:59.992][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:21:59.993][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:21:59.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:21:59.998][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:21:59.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:00.000][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:00.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:22:00.002][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.006][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.010][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.010][private$selectFields]
biodb.TRACE[2024-07-22 21:22:00.011][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-22 21:22:00.012][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-22 21:22:00.013][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.014][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.015][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.017][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.018][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.019][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.020][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.020][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.021][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.022][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.023][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.024][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.025][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.026][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.027][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-22 21:22:00.028][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.032][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.035][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.039][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-07-22 21:22:00.040][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:00.041][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:00.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:00.046][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:00.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:00.048][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:00.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:22:00.050][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.054][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.058][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.059][private$selectFields]
biodb.TRACE[2024-07-22 21:22:00.060][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-22 21:22:00.060][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-22 21:22:00.061][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.062][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.063][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.064][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.065][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.066][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.067][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.068][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.069][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.070][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.071][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.072][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.073][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.073][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.074][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.075][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-22 21:22:00.076][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.080][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.083][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.087][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-07-22 21:22:00.088][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-22 21:22:00.089][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-22 21:22:00.097][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.101][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.105][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.109][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:22:00.115][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:00.116][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:00.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:00.121][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:00.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:00.123][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:00.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:00.126][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[2024-07-22 21:22:00.129][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-22 21:22:00.131][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-07-22 21:22:00.132][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-22 21:22:00.133][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-07-22 21:22:00.136][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[2024-07-22 21:22:00.139][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-22 21:22:00.140][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-07-22 21:22:00.141][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-22 21:22:00.142][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-07-22 21:22:00.151][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:00.152][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:00.153][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:00.157][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:00.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:00.159][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:00.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:22:00.161][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.164][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.168][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:22:00.172][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:00.173][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:00.174][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:00.178][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:00.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:00.179][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:00.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:22:00.181][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.185][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.189][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:22:00.193][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:00.193][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:00.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:00.199][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:00.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:00.201][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:00.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:22:00.203][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.207][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.211][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:22:00.215][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-22 21:22:00.217][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:00.218][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:00.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:00.223][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:00.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:00.225][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:00.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:22:00.227][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.231][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.234][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.235][private$selectFields]
biodb.TRACE[2024-07-22 21:22:00.236][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-22 21:22:00.237][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-22 21:22:00.238][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.239][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.240][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.241][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.242][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.243][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.244][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.244][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.245][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.246][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.247][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.248][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.249][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.250][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.251][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.252][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-22 21:22:00.253][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.256][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.260][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.264][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-07-22 21:22:00.265][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:00.266][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:00.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:00.271][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:00.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:00.273][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:00.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:22:00.275][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.278][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.282][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.283][private$selectFields]
biodb.TRACE[2024-07-22 21:22:00.284][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-22 21:22:00.285][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-22 21:22:00.286][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.286][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.287][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.288][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.289][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.290][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.291][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.292][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.293][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.294][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.295][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.295][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.296][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.297][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.298][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.299][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-22 21:22:00.300][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.312][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.317][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-07-22 21:22:00.318][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:00.319][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:00.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:00.324][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:00.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:00.326][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:00.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:22:00.328][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.332][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.336][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.336][private$selectFields]
biodb.TRACE[2024-07-22 21:22:00.337][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-22 21:22:00.338][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-22 21:22:00.339][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.340][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.341][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.343][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.343][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.344][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.345][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.346][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.347][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.348][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.349][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.350][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.351][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.352][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.352][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-22 21:22:00.353][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.357][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.361][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.365][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-07-22 21:22:00.365][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-22 21:22:00.366][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-22 21:22:00.374][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-07-22 21:22:00.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-07-22 21:22:00.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-22 21:22:00.380][biodb::testThat]
biodb.INFO [2024-07-22 21:22:00.381][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-07-22 21:22:00.382][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-22 21:22:00.383][biodb::testThat]
biodb.TRACE[2024-07-22 21:22:00.385][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-22 21:22:00.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-22 21:22:00.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.389][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:22:00.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:22:00.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.393][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:22:00.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:22:00.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.396][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:22:00.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:22:00.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.400][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:22:00.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:22:00.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:22:00.407][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:00.408][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:00.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:00.413][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:00.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:00.415][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:00.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:00.418][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[2024-07-22 21:22:00.421][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-22 21:22:00.422][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-07-22 21:22:00.424][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-22 21:22:00.425][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-07-22 21:22:00.427][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:00.428][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:00.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:00.433][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:00.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:00.435][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:00.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:22:00.437][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:22:00.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:22:00.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.441][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:22:00.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:22:00.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.444][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:22:00.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:22:00.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:22:00.449][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[2024-07-22 21:22:00.452][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-22 21:22:00.453][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-07-22 21:22:00.454][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-22 21:22:00.455][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-07-22 21:22:00.457][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:00.458][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:00.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:00.463][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:00.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:00.465][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:00.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:22:00.467][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:22:00.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:22:00.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.470][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:22:00.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:22:00.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.480][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:22:00.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:22:00.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:22:00.484][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:00.485][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:00.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:00.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:00.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:00.492][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:00.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:22:00.494][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:22:00.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:22:00.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.498][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:22:00.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:22:00.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.501][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-22 21:22:00.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:22:00.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:22:00.505][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-22 21:22:00.507][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:00.508][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:00.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:00.513][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:00.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:00.514][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:00.515][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[2024-07-22 21:22:00.516][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.520][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.524][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.525][private$selectFields]
biodb.TRACE[2024-07-22 21:22:00.526][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-22 21:22:00.526][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-22 21:22:00.527][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.528][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.529][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.530][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.531][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.532][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.533][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.534][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.535][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.536][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.537][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.537][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.538][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.539][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.540][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.541][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-22 21:22:00.542][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.546][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.549][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.553][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-07-22 21:22:00.554][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:00.555][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:00.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:00.560][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:00.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:00.562][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:00.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:22:00.564][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.568][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.572][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.572][private$selectFields]
biodb.TRACE[2024-07-22 21:22:00.573][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-22 21:22:00.574][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-22 21:22:00.575][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.576][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.577][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.578][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.579][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.580][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.581][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.582][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.582][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.583][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.584][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.585][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.586][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.587][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.588][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.589][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-22 21:22:00.590][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.593][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.597][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.601][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-07-22 21:22:00.602][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:00.603][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:00.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:00.608][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:00.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:00.610][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:00.611][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[2024-07-22 21:22:00.612][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.616][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.619][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.620][private$selectFields]
biodb.TRACE[2024-07-22 21:22:00.621][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-22 21:22:00.622][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-22 21:22:00.623][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.624][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.625][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.626][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.627][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.628][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.629][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.630][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.631][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.631][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.632][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.638][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.639][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.640][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.641][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.642][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-22 21:22:00.643][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.647][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.650][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.654][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-07-22 21:22:00.655][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-22 21:22:00.656][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-22 21:22:00.672][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.676][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.679][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.683][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:22:00.690][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:00.691][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:00.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:00.696][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:00.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:00.697][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:00.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:00.701][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[2024-07-22 21:22:00.704][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-22 21:22:00.705][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-07-22 21:22:00.706][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-22 21:22:00.707][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-07-22 21:22:00.710][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[2024-07-22 21:22:00.713][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-22 21:22:00.714][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-07-22 21:22:00.715][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-22 21:22:00.716][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-07-22 21:22:00.718][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:00.719][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:00.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:00.724][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:00.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:00.726][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:00.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:22:00.727][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.731][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.735][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:22:00.738][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:00.739][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:00.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:00.744][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:00.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:00.746][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:00.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:22:00.748][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.751][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.755][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:22:00.759][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:00.759][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:00.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:00.764][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:00.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:00.766][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:00.767][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.TRACE[2024-07-22 21:22:00.768][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.771][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.775][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:00.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:22:00.779][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-22 21:22:00.780][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:00.781][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:00.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:00.786][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:00.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:00.788][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:00.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:22:00.790][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.799][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.803][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.804][private$selectFields]
biodb.TRACE[2024-07-22 21:22:00.804][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-22 21:22:00.805][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-22 21:22:00.806][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.807][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.808][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.809][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.810][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.811][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.812][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.813][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.814][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.815][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.816][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.817][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.818][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.819][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.819][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.820][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-22 21:22:00.821][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.825][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.829][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.833][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-07-22 21:22:00.834][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:00.835][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:00.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:00.840][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:00.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:00.841][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:00.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:22:00.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.847][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.851][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.851][private$selectFields]
biodb.TRACE[2024-07-22 21:22:00.852][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-22 21:22:00.853][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-22 21:22:00.854][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.855][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.856][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.857][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.858][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.859][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.860][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.860][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.861][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.862][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.863][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.864][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.865][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.866][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.867][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.868][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-22 21:22:00.869][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.872][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.876][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.880][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-07-22 21:22:00.881][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:00.882][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:00.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:00.887][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:00.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:00.888][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:00.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:22:00.890][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.894][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.897][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.898][private$selectFields]
biodb.TRACE[2024-07-22 21:22:00.899][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-22 21:22:00.900][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-22 21:22:00.901][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.902][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.903][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.904][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.905][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.905][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.906][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.907][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.908][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.909][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.910][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-22 21:22:00.911][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.912][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.913][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.914][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.914][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-22 21:22:00.915][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.919][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.923][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:00.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:00.927][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-07-22 21:22:00.928][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-22 21:22:00.928][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-22 21:22:00.945][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-07-22 21:22:00.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-07-22 21:22:00.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:00.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-22 21:22:00.957][biodb::testThat]
biodb.INFO [2024-07-22 21:22:00.958][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2024-07-22 21:22:00.959][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-22 21:22:00.960][biodb::testThat]
biodb.DEBUG[2024-07-22 21:22:00.962][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-07-22 21:22:00.963][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-22 21:22:00.964][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-07-22 21:22:00.965][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-22 21:22:00.966][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-22 21:22:00.967][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-22 21:22:00.968][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-22 21:22:00.969][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-22 21:22:00.970][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-22 21:22:00.973][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:00.974][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:00.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:00.979][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:00.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:00.981][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:00.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:00.983][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-07-22 21:22:00.985][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:22:00.986][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:22:00.987][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-07-22 21:22:01.374][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-07-22 21:22:01.783][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:22:01.785][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-07-22 21:22:01.788][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-07-22 21:22:01.791][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-07-22 21:22:01.793][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-22 21:22:01.794][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-22 21:22:01.795][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-22 21:22:01.797][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:01.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:01.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:01.803][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:01.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:01.805][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:01.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:22:01.808][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:01.809][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:01.810][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:01.811][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:01.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:01.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:01.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:01.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:01.816][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:22:01.817][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:22:01.818][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:01.819][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:01.820][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:22:01.821][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:22:01.822][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:01.823][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:01.825][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:22:01.826][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:22:01.827][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:01.827][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:01.829][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:22:01.830][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:22:01.831][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:01.832][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:01.833][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:22:01.834][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:22:01.835][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:01.836][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:01.837][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:22:01.838][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:22:01.839][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:01.840][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:01.841][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:01.842][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:01.843][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:01.844][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:01.845][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:22:01.846][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:22:01.847][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:01.847][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:01.849][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:22:01.850][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:22:01.851][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:01.851][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:01.853][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:22:01.853][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:22:01.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:01.855][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:01.856][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:01.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:01.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:01.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:01.860][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:01.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:01.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:01.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:01.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:01.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:01.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:01.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:01.867][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:01.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:01.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:01.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:01.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:01.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:01.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:01.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:01.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:01.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:01.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:01.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:01.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:01.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:01.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:01.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:01.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:01.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:01.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:01.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:01.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:01.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:01.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:01.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:01.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:01.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:01.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:01.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:22:01.893][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-07-22 21:22:01.894][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-07-22 21:22:01.901][biodb::testThat]
biodb.INFO [2024-07-22 21:22:01.902][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-07-22 21:22:01.903][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-22 21:22:01.904][biodb::testThat]
biodb.DEBUG[2024-07-22 21:22:01.923][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-07-22 21:22:01.924][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-07-22 21:22:01.925][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-07-22 21:22:01.927][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-07-22 21:22:01.928][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2024-07-22 21:22:01.929][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-22 21:22:01.930][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-22 21:22:01.931][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-22 21:22:01.932][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-22 21:22:01.933][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-22 21:22:01.936][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:01.937][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:01.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:01.943][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:01.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:01.944][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:01.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:01.946][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2024-07-22 21:22:01.949][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:22:01.950][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:22:01.951][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-07-22 21:22:02.338][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-07-22 21:22:02.735][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:22:02.737][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-07-22 21:22:02.740][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-07-22 21:22:02.742][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:02.743][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:02.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:02.749][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:02.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:02.751][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:02.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:02.753][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2024-07-22 21:22:02.756][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:22:02.757][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:22:02.758][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2024-07-22 21:22:03.148][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2024-07-22 21:22:03.542][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:22:03.545][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2024-07-22 21:22:03.550][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2024-07-22 21:22:03.552][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:03.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:03.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:03.562][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:03.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:03.564][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:03.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:03.567][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2024-07-22 21:22:03.571][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:22:03.573][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:22:03.574][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-07-22 21:22:03.992][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2024-07-22 21:22:04.383][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:22:04.385][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-07-22 21:22:04.388][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-07-22 21:22:04.391][private$doSaveContentToFile] Saving to cache [3]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2024-07-22 21:22:04.393][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-22 21:22:04.394][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-07-22 21:22:04.395][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-07-22 21:22:04.397][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:04.398][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:04.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:04.403][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:04.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:04.405][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:04.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:22:04.408][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:04.409][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:04.410][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.411][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:04.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:04.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.417][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:22:04.418][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:22:04.419][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.420][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.421][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:22:04.422][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:22:04.423][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.424][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.425][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:22:04.426][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:22:04.427][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.428][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.429][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:22:04.430][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:22:04.431][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.432][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.434][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:22:04.435][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:22:04.436][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.436][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.438][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:22:04.439][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:22:04.440][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.441][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.442][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:04.443][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:04.444][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.445][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.446][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:22:04.447][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:22:04.448][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.449][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.450][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:22:04.451][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:22:04.452][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.453][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.454][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:22:04.455][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:22:04.456][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.457][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.458][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:04.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:04.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.461][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:04.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:04.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:04.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:04.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.484][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:04.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:04.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:04.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:04.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.492][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:04.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:04.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:04.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:04.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:22:04.499][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:04.500][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:04.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:04.505][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:04.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:04.507][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:04.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:22:04.510][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:04.511][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:04.512][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.513][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:04.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:04.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.518][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:22:04.519][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:22:04.520][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.521][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.522][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:22:04.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:22:04.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.526][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:22:04.527][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:22:04.528][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.529][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.530][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:22:04.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:22:04.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.534][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:22:04.535][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:22:04.536][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.537][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.538][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:22:04.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:22:04.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.542][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:22:04.543][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:22:04.544][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.545][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.546][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:22:04.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:22:04.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.550][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:22:04.551][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:22:04.552][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.553][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.554][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:22:04.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:22:04.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.558][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:22:04.559][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:22:04.560][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.561][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.562][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:22:04.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:22:04.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.566][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:04.567][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:04.568][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.569][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.570][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:04.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:04.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.574][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:22:04.575][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:22:04.576][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.577][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.578][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:22:04.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:22:04.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.582][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:22:04.583][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:22:04.584][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.585][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.586][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:22:04.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:22:04.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.590][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:22:04.591][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:22:04.592][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.593][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.594][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:22:04.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:22:04.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.598][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:04.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:04.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.602][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:04.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:04.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:04.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:04.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.609][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:04.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:04.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:04.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:04.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:04.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:04.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:04.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:04.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:22:04.624][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:04.625][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:04.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:04.630][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:04.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:04.632][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:04.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:22:04.635][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:04.636][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:04.637][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.638][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:04.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:04.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.649][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:22:04.650][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:22:04.651][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.652][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.653][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:22:04.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:22:04.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.657][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:22:04.658][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:22:04.659][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.659][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.661][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:22:04.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:22:04.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.665][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:22:04.666][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:22:04.666][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.667][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.669][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:22:04.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:22:04.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.672][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:22:04.673][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:22:04.674][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.675][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.676][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:22:04.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:22:04.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.680][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:22:04.681][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:22:04.682][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.683][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.684][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:22:04.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:22:04.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.688][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:22:04.689][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:22:04.690][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.691][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.692][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:22:04.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:22:04.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.696][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:04.697][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:04.698][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.699][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.700][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:04.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:04.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.704][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:22:04.705][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:22:04.705][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.706][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.708][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:22:04.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:22:04.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.712][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:22:04.712][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:22:04.713][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.714][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.715][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:22:04.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:22:04.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.719][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:22:04.720][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:22:04.721][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.722][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.723][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:22:04.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:22:04.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.727][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:04.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:04.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.731][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:04.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:04.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:04.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:04.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.738][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:04.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:04.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:04.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:04.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:04.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:04.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:04.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:04.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:04.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:04.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:04.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:04.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:04.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:04.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:04.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:04.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:04.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:04.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:04.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:04.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:04.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:04.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:04.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:04.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:04.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:04.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:04.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:04.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:22:04.786][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-07-22 21:22:04.787][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-07-22 21:22:04.788][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-07-22 21:22:04.805][biodb::testThat]
biodb.INFO [2024-07-22 21:22:04.806][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2024-07-22 21:22:04.808][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-22 21:22:04.809][biodb::testThat]
biodb.INFO [2024-07-22 21:22:04.831][biodb::testThat]
biodb.INFO [2024-07-22 21:22:04.832][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2024-07-22 21:22:04.833][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-22 21:22:04.834][biodb::testThat]
biodb.INFO [2024-07-22 21:22:04.841][biodb::testThat]
biodb.INFO [2024-07-22 21:22:04.842][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2024-07-22 21:22:04.843][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-22 21:22:04.843][biodb::testThat]
biodb.DEBUG[2024-07-22 21:22:04.846][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[2024-07-22 21:22:04.849][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:22:04.850][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:22:04.852][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2024-07-22 21:22:05.301][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2024-07-22 21:22:05.826][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:22:05.829][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-07-22 21:22:05.835][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-07-22 21:22:05.854][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:22:05.856][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:22:05.857][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:05.859][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:05.861][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:05.862][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:05.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:05.865][ef$get] fields variable is a list.
biodb.INFO [2024-07-22 21:22:05.868][biodb::testThat]
biodb.INFO [2024-07-22 21:22:05.869][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2024-07-22 21:22:05.871][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-22 21:22:05.872][biodb::testThat]
biodb.ERROR[2024-07-22 21:22:05.896][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-07-22 21:22:05.924][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-07-22 21:22:05.946][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-22 21:22:05.948][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-07-22 21:22:05.950][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-07-22 21:22:05.951][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-22 21:22:05.952][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:05.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:05.955][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:05.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:05.957][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:05.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-07-22 21:22:05.975][biodb::testContext]
biodb.INFO [2024-07-22 21:22:05.977][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-22 21:22:05.978][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-07-22 21:22:05.980][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-22 21:22:05.981][biodb::testContext]
biodb.INFO [2024-07-22 21:22:05.984][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-07-22 21:22:05.987][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-07-22 21:22:05.992][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-22 21:22:05.993][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-22 21:22:05.995][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-22 21:22:05.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:05.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:05.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.000][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-22 21:22:06.002][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-22 21:22:06.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.016][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-22 21:22:06.023][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-22 21:22:06.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.029][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-22 21:22:06.031][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-22 21:22:06.032][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-22 21:22:06.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.037][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-22 21:22:06.039][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-22 21:22:06.040][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-22 21:22:06.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.044][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-22 21:22:06.045][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-22 21:22:06.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.048][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-22 21:22:06.049][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-22 21:22:06.050][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-22 21:22:06.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.053][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-22 21:22:06.054][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-22 21:22:06.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.058][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-22 21:22:06.059][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-22 21:22:06.060][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-22 21:22:06.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.063][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-22 21:22:06.064][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-22 21:22:06.065][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-22 21:22:06.066][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-22 21:22:06.067][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-22 21:22:06.068][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-22 21:22:06.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.071][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-22 21:22:06.073][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-22 21:22:06.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.077][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-22 21:22:06.078][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-22 21:22:06.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.082][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-22 21:22:06.083][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-22 21:22:06.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.086][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-22 21:22:06.087][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-22 21:22:06.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.091][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-22 21:22:06.092][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-22 21:22:06.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.095][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-22 21:22:06.096][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-22 21:22:06.100][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-22 21:22:06.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.104][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-22 21:22:06.105][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-22 21:22:06.106][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-22 21:22:06.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.109][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-22 21:22:06.111][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:06.112][self$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[2024-07-22 21:22:06.113][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:06.114][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-22 21:22:06.115][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:06.116][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-22 21:22:06.117][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:06.118][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-22 21:22:06.118][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-22 21:22:06.119][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-22 21:22:06.120][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:06.121][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-22 21:22:06.122][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-22 21:22:06.123][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:06.124][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:06.125][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-22 21:22:06.125][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-22 21:22:06.125][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-22 21:22:06.125][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-22 21:22:06.125][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-22 21:22:06.126][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-22 21:22:06.127][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:22:06.128][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:22:06.129][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-22 21:22:06.130][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:22:06.131][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:22:06.132][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-22 21:22:06.132][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:06.133][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-22 21:22:06.134][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-22 21:22:06.135][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:06.136][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:06.137][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-22 21:22:06.139][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:06.141][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-22 21:22:06.142][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:06.143][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-22 21:22:06.145][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:06.146][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-22 21:22:06.147][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:06.148][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-22 21:22:06.148][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-22 21:22:06.149][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-22 21:22:06.150][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:06.151][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-22 21:22:06.152][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-22 21:22:06.153][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:06.154][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:06.155][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-22 21:22:06.155][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-22 21:22:06.155][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-22 21:22:06.155][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-22 21:22:06.155][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-22 21:22:06.156][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-22 21:22:06.157][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:22:06.158][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:22:06.159][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-22 21:22:06.159][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:22:06.160][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:22:06.161][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-22 21:22:06.162][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:06.163][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-22 21:22:06.164][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-22 21:22:06.165][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:06.166][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:06.167][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-22 21:22:06.168][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:06.169][self$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[2024-07-22 21:22:06.170][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:06.171][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-22 21:22:06.172][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:06.173][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-22 21:22:06.174][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:06.175][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-22 21:22:06.176][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-22 21:22:06.177][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-22 21:22:06.178][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:06.178][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-22 21:22:06.179][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-22 21:22:06.180][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:06.181][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:06.182][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:06.183][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-22 21:22:06.184][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:22:06.383][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:22:06.385][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-22 21:22:06.386][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:22:06.387][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:22:06.388][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-22 21:22:06.388][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:06.389][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-22 21:22:06.390][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-22 21:22:06.391][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:06.392][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:06.393][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-22 21:22:06.394][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:06.395][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-22 21:22:06.396][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:06.397][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-22 21:22:06.398][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:06.399][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-22 21:22:06.400][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:06.401][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-22 21:22:06.402][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-22 21:22:06.403][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-22 21:22:06.404][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:06.405][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-22 21:22:06.406][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-22 21:22:06.407][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:06.407][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:06.408][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:06.409][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-22 21:22:06.410][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:22:06.411][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:22:06.412][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-22 21:22:06.413][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:22:06.413][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:22:06.414][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-22 21:22:06.415][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:06.416][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-22 21:22:06.417][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-22 21:22:06.417][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:06.418][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:06.420][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-22 21:22:06.420][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.441][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[2024-07-22 21:22:06.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.452][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.DEBUG[2024-07-22 21:22:06.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.488][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[2024-07-22 21:22:06.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.493][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-22 21:22:06.494][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-22 21:22:06.495][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-22 21:22:06.496][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-22 21:22:06.498][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-22 21:22:06.499][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-22 21:22:06.500][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-22 21:22:06.501][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-22 21:22:06.503][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-22 21:22:06.504][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-22 21:22:06.505][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-22 21:22:06.507][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-22 21:22:06.508][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-22 21:22:06.509][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-22 21:22:06.510][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-22 21:22:06.512][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-22 21:22:06.513][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-22 21:22:06.514][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-22 21:22:06.515][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-22 21:22:06.517][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-22 21:22:06.518][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-22 21:22:06.519][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-22 21:22:06.521][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-22 21:22:06.522][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-22 21:22:06.523][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-22 21:22:06.524][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-22 21:22:06.526][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-22 21:22:06.527][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-22 21:22:06.528][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-22 21:22:06.529][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-22 21:22:06.531][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-22 21:22:06.532][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-22 21:22:06.533][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-22 21:22:06.534][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-22 21:22:06.536][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-22 21:22:06.541][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-22 21:22:06.542][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-22 21:22:06.544][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-22 21:22:06.545][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-22 21:22:06.546][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-22 21:22:06.547][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-22 21:22:06.548][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-22 21:22:06.550][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-22 21:22:06.551][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-22 21:22:06.552][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-22 21:22:06.553][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-22 21:22:06.555][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-22 21:22:06.556][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-22 21:22:06.557][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-22 21:22:06.558][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-22 21:22:06.560][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-22 21:22:06.561][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-22 21:22:06.562][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-22 21:22:06.563][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-22 21:22:06.565][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-22 21:22:06.566][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-22 21:22:06.567][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-22 21:22:06.568][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-22 21:22:06.570][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-22 21:22:06.571][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-22 21:22:06.572][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-22 21:22:06.573][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-22 21:22:06.574][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-22 21:22:06.576][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-22 21:22:06.577][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-22 21:22:06.578][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-22 21:22:06.579][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-22 21:22:06.580][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-22 21:22:06.582][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-22 21:22:06.583][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-22 21:22:06.584][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-22 21:22:06.585][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-22 21:22:06.587][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-22 21:22:06.588][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-22 21:22:06.589][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-22 21:22:06.590][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-22 21:22:06.591][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-22 21:22:06.593][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-22 21:22:06.594][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-22 21:22:06.595][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-22 21:22:06.597][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-22 21:22:06.598][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-22 21:22:06.599][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-22 21:22:06.601][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-22 21:22:06.603][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-07-22 21:22:06.603][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-22 21:22:06.604][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.606][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:06.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:06.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:06.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:06.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:06.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:06.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.623][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[2024-07-22 21:22:06.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:06.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:06.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:06.632][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:06.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:06.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:06.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.642][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[2024-07-22 21:22:06.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:06.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:06.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.648][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[2024-07-22 21:22:06.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:06.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:06.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.654][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[2024-07-22 21:22:06.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:06.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:06.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.660][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[2024-07-22 21:22:06.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:06.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:06.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:06.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:06.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:06.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:06.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.679][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[2024-07-22 21:22:06.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:06.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:06.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:06.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:06.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:06.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:06.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:06.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:06.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:06.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:06.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:06.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:06.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:06.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:06.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:06.721][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-07-22 21:22:06.722][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-07-22 21:22:06.725][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:06.727][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-22 21:22:06.729][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:06.730][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-22 21:22:06.732][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:06.733][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-22 21:22:06.734][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:06.736][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-07-22 21:22:06.737][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-07-22 21:22:06.739][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-22 21:22:06.740][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:06.741][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-07-22 21:22:06.742][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-22 21:22:06.744][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-07-22 21:22:06.744][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-07-22 21:22:06.744][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-07-22 21:22:06.744][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-07-22 21:22:06.744][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-07-22 21:22:06.744][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-07-22 21:22:06.744][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-07-22 21:22:06.744][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-07-22 21:22:06.744][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-07-22 21:22:06.744][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-07-22 21:22:06.744][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-07-22 21:22:06.745][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:06.745][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-22 21:22:06.745][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-22 21:22:06.745][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-22 21:22:06.746][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-22 21:22:06.747][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:22:06.748][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:22:06.749][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-22 21:22:06.750][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:22:06.751][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:22:06.752][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-22 21:22:06.754][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-22 21:22:06.754][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-07-22 21:22:06.755][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-22 21:22:06.756][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-22 21:22:06.757][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:06.758][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-07-22 21:22:06.758][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-07-22 21:22:06.760][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-22 21:22:06.762][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-22 21:22:06.764][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-07-22 21:22:06.765][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-22 21:22:06.768][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-22 21:22:06.770][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-22 21:22:06.774][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-07-22 21:22:06.775][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-07-22 21:22:06.777][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-07-22 21:22:06.778][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-07-22 21:22:06.779][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-22 21:22:06.780][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-22 21:22:06.781][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-07-22 21:22:06.782][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-07-22 21:22:06.784][biodb::testThat]
biodb.INFO [2024-07-22 21:22:06.785][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2024-07-22 21:22:06.785][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-22 21:22:06.786][biodb::testThat]
biodb.DEBUG[2024-07-22 21:22:06.790][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-07-22 21:22:06.794][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:22:06.795][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:22:06.797][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2024-07-22 21:22:07.192][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2024-07-22 21:22:07.761][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:22:07.764][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2024-07-22 21:22:07.770][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2024-07-22 21:22:07.777][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[2024-07-22 21:22:07.783][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:22:07.785][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:22:07.788][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-07-22 21:22:08.240][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-07-22 21:22:08.639][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:22:08.642][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2024-07-22 21:22:08.648][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2024-07-22 21:22:08.652][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:08.653][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:08.655][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:08.661][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:08.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:08.665][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:08.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:08.671][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-22 21:22:08.679][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:22:08.681][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:22:08.684][private$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[2024-07-22 21:22:09.114][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[2024-07-22 21:22:09.593][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:22:09.597][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2024-07-22 21:22:09.620][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2024-07-22 21:22:09.623][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:09.648][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:09.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:09.656][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:09.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:09.658][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:09.659][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[2024-07-22 21:22:09.711][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:09.712][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:09.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:09.777][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:09.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:09.780][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:09.781][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[2024-07-22 21:22:09.787][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[2024-07-22 21:22:09.799][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-22 21:22:09.801][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-07-22 21:22:09.803][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-22 21:22:09.804][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-07-22 21:22:09.806][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:09.807][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:09.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:09.831][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:09.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:09.833][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:09.834][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[2024-07-22 21:22:09.837][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[2024-07-22 21:22:09.841][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-22 21:22:09.843][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-07-22 21:22:09.845][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-22 21:22:09.847][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-07-22 21:22:09.849][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:09.851][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:09.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:09.859][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:09.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:09.862][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:09.864][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[2024-07-22 21:22:09.865][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:09.867][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:09.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:09.875][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:09.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:09.878][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:09.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:09.886][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[2024-07-22 21:22:09.891][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-22 21:22:09.893][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-07-22 21:22:09.895][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-22 21:22:09.897][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-07-22 21:22:09.899][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:09.901][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:09.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:09.909][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:09.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:09.912][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:09.913][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[2024-07-22 21:22:09.916][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[2024-07-22 21:22:09.921][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-22 21:22:09.924][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-07-22 21:22:09.926][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-22 21:22:09.928][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-07-22 21:22:09.931][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:09.932][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:09.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:09.941][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:09.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:09.944][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:09.946][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[2024-07-22 21:22:09.949][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[2024-07-22 21:22:09.954][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:22:09.956][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:22:09.960][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-07-22 21:22:10.380][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-07-22 21:22:10.786][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:22:10.790][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2024-07-22 21:22:10.796][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2024-07-22 21:22:10.800][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:10.802][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:10.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:10.811][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:10.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:10.814][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:10.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-07-22 21:22:10.826][biodb::testThat]
biodb.INFO [2024-07-22 21:22:10.828][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2024-07-22 21:22:10.830][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-22 21:22:10.831][biodb::testThat]
biodb.DEBUG[2024-07-22 21:22:10.837][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-22 21:22:10.843][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:22:10.845][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:22:10.848][private$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[2024-07-22 21:22:11.277][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[2024-07-22 21:22:11.695][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:22:11.699][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-07-22 21:22:11.706][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-07-22 21:22:11.710][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:11.712][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:11.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:11.722][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:11.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:11.726][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:11.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:11.736][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[2024-07-22 21:22:11.742][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:22:11.744][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:22:11.748][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-07-22 21:22:12.186][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-07-22 21:22:12.603][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:22:12.607][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-07-22 21:22:12.614][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-07-22 21:22:12.618][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:12.620][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:12.622][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:12.630][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:12.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:12.634][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:12.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-07-22 21:22:12.645][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-22 21:22:12.647][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-07-22 21:22:12.649][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-07-22 21:22:12.651][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-22 21:22:12.652][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:12.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:12.655][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:12.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:12.658][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:12.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-07-22 21:22:12.666][biodb::testContext]
biodb.INFO [2024-07-22 21:22:12.668][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-22 21:22:12.669][biodb::testContext] Test context - Test web services
biodb.INFO [2024-07-22 21:22:12.671][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-22 21:22:12.673][biodb::testContext]
biodb.INFO [2024-07-22 21:22:12.676][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-07-22 21:22:12.679][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-07-22 21:22:12.685][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-22 21:22:12.687][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-22 21:22:12.688][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-22 21:22:12.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:12.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:12.693][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[2024-07-22 21:22:12.694][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-22 21:22:12.696][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-22 21:22:12.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:12.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:12.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:12.701][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-22 21:22:12.703][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-22 21:22:12.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:12.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:12.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:12.709][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-22 21:22:12.710][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-22 21:22:12.712][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-22 21:22:12.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:12.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:12.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:12.717][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-22 21:22:12.719][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-22 21:22:12.720][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-22 21:22:12.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:12.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:12.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:12.726][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-22 21:22:12.728][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-22 21:22:12.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:12.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:12.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:12.733][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-22 21:22:12.735][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-22 21:22:12.737][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-22 21:22:12.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:12.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:12.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:12.742][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-22 21:22:12.744][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-22 21:22:12.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:12.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:12.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:12.749][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-22 21:22:12.751][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-22 21:22:12.753][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-22 21:22:12.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:12.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:12.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:12.758][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-22 21:22:12.760][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-22 21:22:12.761][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-22 21:22:12.763][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-22 21:22:12.764][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-22 21:22:12.766][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-22 21:22:12.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:12.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:12.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:12.772][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-22 21:22:12.773][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-22 21:22:12.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:12.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:12.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:12.779][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-22 21:22:12.781][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-22 21:22:12.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:12.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:12.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:12.786][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-22 21:22:12.788][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-22 21:22:12.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:12.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:12.792][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[2024-07-22 21:22:12.793][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-22 21:22:12.795][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-22 21:22:12.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:12.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:12.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:12.799][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-22 21:22:12.800][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-22 21:22:12.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:12.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:12.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:12.803][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-22 21:22:12.804][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-22 21:22:12.808][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-22 21:22:12.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:12.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:12.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:12.812][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-22 21:22:12.813][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-22 21:22:12.814][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-22 21:22:12.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:12.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:12.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:12.818][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-22 21:22:12.821][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:12.822][self$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[2024-07-22 21:22:12.823][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:12.824][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-22 21:22:12.825][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:12.826][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-22 21:22:12.827][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:12.828][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-22 21:22:12.829][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-22 21:22:12.830][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-22 21:22:12.831][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:12.832][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-22 21:22:12.833][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-22 21:22:12.834][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:12.836][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:12.837][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-22 21:22:12.837][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-22 21:22:12.837][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-22 21:22:12.837][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-22 21:22:12.837][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-22 21:22:12.838][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-22 21:22:12.839][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:22:12.840][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:22:12.841][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-22 21:22:12.842][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:22:12.843][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:22:12.844][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-22 21:22:12.845][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:12.846][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-22 21:22:12.847][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-22 21:22:12.848][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:12.849][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:12.850][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-22 21:22:12.862][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:12.864][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-22 21:22:12.865][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:12.866][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-22 21:22:12.867][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:12.868][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-22 21:22:12.869][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:12.871][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-22 21:22:12.872][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-22 21:22:12.873][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-22 21:22:12.874][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:12.875][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-22 21:22:12.876][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-22 21:22:12.877][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:12.878][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:12.879][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-22 21:22:12.879][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-22 21:22:12.879][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-22 21:22:12.879][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-22 21:22:12.879][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-22 21:22:12.880][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-22 21:22:12.881][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:22:12.882][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:22:12.884][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-22 21:22:12.885][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:22:12.886][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:22:12.887][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-22 21:22:12.888][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:12.889][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-22 21:22:12.890][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-22 21:22:12.891][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:12.893][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:12.895][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-22 21:22:12.898][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:12.899][self$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[2024-07-22 21:22:12.901][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:12.902][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-22 21:22:12.904][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:12.905][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-22 21:22:12.907][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:12.908][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-22 21:22:12.909][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-22 21:22:12.910][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-22 21:22:12.911][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:12.912][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-22 21:22:12.913][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-22 21:22:12.914][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:12.915][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:12.916][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:12.917][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-22 21:22:12.918][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:22:12.919][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:22:12.921][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-22 21:22:12.922][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:22:12.923][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:22:12.924][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-22 21:22:12.925][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:12.926][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-22 21:22:12.926][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-22 21:22:12.927][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:12.928][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:12.929][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-22 21:22:12.931][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:12.932][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-22 21:22:12.933][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:12.934][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-22 21:22:12.935][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:12.936][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-22 21:22:12.938][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:12.939][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-22 21:22:12.940][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-22 21:22:12.941][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-22 21:22:12.942][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:12.943][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-22 21:22:12.944][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-22 21:22:12.945][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:12.946][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:12.948][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:12.949][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-22 21:22:12.950][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:22:12.951][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:22:12.952][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-22 21:22:12.953][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:22:12.954][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:22:12.955][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-22 21:22:12.956][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:12.957][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-22 21:22:12.958][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-22 21:22:12.959][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:12.960][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:12.961][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-22 21:22:12.962][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:12.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:12.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:12.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:12.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:12.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:12.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:12.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:12.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:12.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:12.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:12.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:12.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:12.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:12.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:12.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:12.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:12.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:12.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:12.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:12.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:12.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:12.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:12.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:12.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:12.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:12.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:12.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:12.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:12.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:12.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:12.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:12.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:12.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:12.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:12.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:12.995][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.DEBUG[2024-07-22 21:22:12.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:12.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:12.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:12.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:13.000][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[2024-07-22 21:22:13.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:13.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:13.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:13.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:13.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:13.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:13.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:13.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:13.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:13.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:13.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:13.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:13.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:13.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:13.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:13.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:13.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:13.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:13.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:13.020][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[2024-07-22 21:22:13.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:13.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:13.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:13.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:13.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:13.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:13.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:13.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:13.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:13.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:13.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:13.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:13.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:13.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:13.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:13.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:13.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:13.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:13.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:13.040][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[2024-07-22 21:22:13.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:13.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:13.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:13.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:13.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:13.053][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-22 21:22:13.056][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-22 21:22:13.058][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-22 21:22:13.060][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-22 21:22:13.062][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-22 21:22:13.064][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-22 21:22:13.066][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-22 21:22:13.069][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-22 21:22:13.071][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-22 21:22:13.073][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-22 21:22:13.074][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-22 21:22:13.075][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-22 21:22:13.077][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-22 21:22:13.078][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-22 21:22:13.080][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-22 21:22:13.082][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-22 21:22:13.084][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-22 21:22:13.087][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-22 21:22:13.089][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-22 21:22:13.091][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-22 21:22:13.093][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-22 21:22:13.095][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-22 21:22:13.097][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-22 21:22:13.099][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-22 21:22:13.101][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-22 21:22:13.102][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-22 21:22:13.103][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-22 21:22:13.104][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-22 21:22:13.106][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-22 21:22:13.107][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-22 21:22:13.108][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-22 21:22:13.110][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-22 21:22:13.113][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-22 21:22:13.115][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-22 21:22:13.117][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-22 21:22:13.119][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-22 21:22:13.122][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-22 21:22:13.124][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-22 21:22:13.126][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-22 21:22:13.128][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-22 21:22:13.130][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-22 21:22:13.132][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-22 21:22:13.135][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-22 21:22:13.137][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-22 21:22:13.139][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-22 21:22:13.141][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-22 21:22:13.142][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-22 21:22:13.145][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-22 21:22:13.147][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-22 21:22:13.149][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-22 21:22:13.151][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-22 21:22:13.153][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-22 21:22:13.155][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-22 21:22:13.158][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-22 21:22:13.160][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-22 21:22:13.161][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-22 21:22:13.163][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-22 21:22:13.164][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-22 21:22:13.166][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-22 21:22:13.168][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-22 21:22:13.170][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-22 21:22:13.172][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-22 21:22:13.174][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-22 21:22:13.176][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-22 21:22:13.179][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-22 21:22:13.181][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-22 21:22:13.183][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-22 21:22:13.185][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-22 21:22:13.187][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-22 21:22:13.189][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-22 21:22:13.192][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-22 21:22:13.193][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-22 21:22:13.195][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-22 21:22:13.196][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-22 21:22:13.198][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-22 21:22:13.200][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-22 21:22:13.202][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-22 21:22:13.204][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-22 21:22:13.206][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-22 21:22:13.209][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-22 21:22:13.211][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-22 21:22:13.213][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-22 21:22:13.215][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-22 21:22:13.217][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-22 21:22:13.218][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-07-22 21:22:13.219][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-22 21:22:13.221][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:13.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:13.223][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:13.224][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.DEBUG[2024-07-22 21:22:13.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:13.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:13.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:13.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:13.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:13.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:13.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:13.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:13.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:13.233][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:13.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:13.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:13.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:13.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:13.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:13.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:13.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:13.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:13.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:13.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:13.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:13.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:13.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:13.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:13.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:13.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:13.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:13.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:13.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:13.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:13.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:13.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:13.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:13.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:13.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:13.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:13.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:13.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:13.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:13.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:13.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:13.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:13.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:13.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:13.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:13.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:13.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:13.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:13.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:13.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:13.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:13.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:13.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:13.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:13.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:13.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:13.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:13.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:13.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:13.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:13.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:13.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:13.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:13.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:13.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:13.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:13.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:13.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:13.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:13.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:13.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:13.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:13.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:13.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:13.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:13.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:13.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:13.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:13.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:13.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:13.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:13.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:13.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:13.332][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.DEBUG[2024-07-22 21:22:13.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:13.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:13.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:13.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:13.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:13.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:13.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:13.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:13.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:13.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:13.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:13.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:13.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:13.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:13.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:13.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:13.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:13.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:13.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:13.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:13.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:13.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:13.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:13.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:13.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:13.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:13.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:13.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:13.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:13.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:13.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:13.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:13.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:13.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:13.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:13.367][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-07-22 21:22:13.368][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-07-22 21:22:13.370][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:13.371][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-22 21:22:13.372][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:13.373][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-22 21:22:13.375][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:13.376][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-22 21:22:13.377][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:13.378][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-07-22 21:22:13.379][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-07-22 21:22:13.380][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-22 21:22:13.381][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:13.382][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-07-22 21:22:13.383][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-22 21:22:13.384][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-07-22 21:22:13.384][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-07-22 21:22:13.384][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-07-22 21:22:13.384][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-07-22 21:22:13.384][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-07-22 21:22:13.384][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-07-22 21:22:13.384][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-07-22 21:22:13.384][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-07-22 21:22:13.384][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-07-22 21:22:13.384][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-07-22 21:22:13.384][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-07-22 21:22:13.385][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:13.386][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-22 21:22:13.386][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-22 21:22:13.386][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-22 21:22:13.387][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-22 21:22:13.388][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:22:13.389][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:22:13.390][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-22 21:22:13.391][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:22:13.392][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:22:13.393][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-22 21:22:13.394][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-22 21:22:13.394][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-07-22 21:22:13.395][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-22 21:22:13.396][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-22 21:22:13.397][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:13.398][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-07-22 21:22:13.398][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-07-22 21:22:13.400][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-22 21:22:13.402][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-22 21:22:13.405][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-07-22 21:22:13.407][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-22 21:22:13.409][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-22 21:22:13.412][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-22 21:22:13.417][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-07-22 21:22:13.419][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-07-22 21:22:13.421][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-07-22 21:22:13.423][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-07-22 21:22:13.425][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-22 21:22:13.427][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-22 21:22:13.429][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-07-22 21:22:13.430][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-07-22 21:22:13.432][biodb::testThat]
biodb.INFO [2024-07-22 21:22:13.434][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-07-22 21:22:13.435][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-22 21:22:13.437][biodb::testThat]
biodb.DEBUG[2024-07-22 21:22:13.441][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-07-22 21:22:13.447][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-22 21:22:13.449][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-07-22 21:22:13.451][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-22 21:22:13.453][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-07-22 21:22:13.459][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-22 21:22:13.464][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:22:13.466][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:22:13.468][private$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[2024-07-22 21:22:13.893][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[2024-07-22 21:22:14.301][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:22:14.304][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-07-22 21:22:14.308][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-07-22 21:22:14.316][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-22 21:22:14.318][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-07-22 21:22:14.319][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-07-22 21:22:14.330][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-22 21:22:14.331][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:14.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:14.333][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.335][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.336][FUN] Functions in observer BiodbConfig: [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 [2024-07-22 21:22:14.340][biodb::testContext]
biodb.INFO [2024-07-22 21:22:14.341][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-22 21:22:14.342][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-07-22 21:22:14.343][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-22 21:22:14.344][biodb::testContext]
biodb.INFO [2024-07-22 21:22:14.346][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-07-22 21:22:14.348][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-07-22 21:22:14.352][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-22 21:22:14.353][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-22 21:22:14.354][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-22 21:22:14.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.357][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-22 21:22:14.358][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-22 21:22:14.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.361][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[2024-07-22 21:22:14.362][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-22 21:22:14.363][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-22 21:22:14.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.366][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-22 21:22:14.367][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-22 21:22:14.368][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-22 21:22:14.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.371][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-22 21:22:14.372][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-22 21:22:14.373][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-22 21:22:14.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.376][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-22 21:22:14.377][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-22 21:22:14.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.381][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-22 21:22:14.381][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-22 21:22:14.382][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-22 21:22:14.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.386][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-22 21:22:14.387][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-22 21:22:14.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.390][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-22 21:22:14.391][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-22 21:22:14.392][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-22 21:22:14.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.395][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-22 21:22:14.396][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-22 21:22:14.397][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-22 21:22:14.398][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-22 21:22:14.399][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-22 21:22:14.400][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-22 21:22:14.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.403][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[2024-07-22 21:22:14.403][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-22 21:22:14.404][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-22 21:22:14.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.408][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-22 21:22:14.409][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-22 21:22:14.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.412][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-22 21:22:14.413][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-22 21:22:14.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.416][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-22 21:22:14.417][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-22 21:22:14.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.421][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-22 21:22:14.421][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-22 21:22:14.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.425][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-22 21:22:14.426][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-22 21:22:14.429][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-22 21:22:14.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.432][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[2024-07-22 21:22:14.432][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-22 21:22:14.433][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-22 21:22:14.434][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-22 21:22:14.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.438][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-22 21:22:14.439][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:14.440][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-22 21:22:14.441][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:14.442][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-22 21:22:14.443][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:14.444][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-22 21:22:14.445][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:14.446][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-22 21:22:14.447][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-22 21:22:14.447][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-22 21:22:14.448][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:14.449][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-22 21:22:14.450][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-22 21:22:14.451][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:14.452][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:14.453][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-22 21:22:14.453][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-22 21:22:14.453][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-22 21:22:14.453][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-22 21:22:14.453][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-22 21:22:14.454][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-22 21:22:14.455][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:22:14.456][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:22:14.456][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-22 21:22:14.457][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:22:14.458][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:22:14.459][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-22 21:22:14.460][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:14.461][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-22 21:22:14.462][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-22 21:22:14.463][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:14.463][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:14.465][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-22 21:22:14.466][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:14.467][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-22 21:22:14.468][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:14.469][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-22 21:22:14.470][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:14.471][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-22 21:22:14.472][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:14.473][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-22 21:22:14.474][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-22 21:22:14.474][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-22 21:22:14.475][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:14.476][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-22 21:22:14.477][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-22 21:22:14.478][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:14.479][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:14.480][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-22 21:22:14.480][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-22 21:22:14.480][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-22 21:22:14.480][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-22 21:22:14.480][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-22 21:22:14.481][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-22 21:22:14.482][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:22:14.483][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:22:14.484][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-22 21:22:14.484][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:22:14.485][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:22:14.491][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-22 21:22:14.492][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:14.493][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-22 21:22:14.494][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-22 21:22:14.494][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:14.495][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:14.496][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-22 21:22:14.498][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:14.499][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-22 21:22:14.500][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:14.501][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-22 21:22:14.502][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:14.502][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-22 21:22:14.503][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:14.504][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-22 21:22:14.505][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-22 21:22:14.506][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-22 21:22:14.507][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:14.508][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-22 21:22:14.509][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-22 21:22:14.510][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:14.510][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:14.511][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:14.512][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-22 21:22:14.513][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:22:14.514][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:22:14.515][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-22 21:22:14.516][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:22:14.516][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:22:14.517][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-22 21:22:14.518][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:14.519][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-22 21:22:14.520][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-22 21:22:14.521][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:14.522][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:14.523][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-22 21:22:14.524][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:14.525][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-22 21:22:14.526][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:14.527][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-22 21:22:14.528][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:14.529][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-22 21:22:14.530][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:14.530][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-22 21:22:14.531][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-22 21:22:14.532][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-22 21:22:14.533][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:14.534][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-22 21:22:14.535][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-22 21:22:14.536][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:14.537][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:14.538][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:14.538][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-22 21:22:14.539][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:22:14.540][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:22:14.541][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-22 21:22:14.542][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:22:14.543][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:22:14.543][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-22 21:22:14.544][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:14.545][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-22 21:22:14.546][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-22 21:22:14.547][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:14.548][self$setPropertyValue]
biodb.DEBUG[2024-07-22 21:22:14.549][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-22 21:22:14.550][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.611][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.DEBUG[2024-07-22 21:22:14.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.620][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-22 21:22:14.621][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-22 21:22:14.622][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-22 21:22:14.624][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-22 21:22:14.625][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-22 21:22:14.626][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-22 21:22:14.627][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-22 21:22:14.629][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-22 21:22:14.630][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-22 21:22:14.631][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-22 21:22:14.633][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-22 21:22:14.634][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-22 21:22:14.640][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-22 21:22:14.641][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-22 21:22:14.643][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-22 21:22:14.644][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-22 21:22:14.645][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-22 21:22:14.646][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-22 21:22:14.648][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-22 21:22:14.649][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-22 21:22:14.650][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-22 21:22:14.651][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-22 21:22:14.653][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-22 21:22:14.654][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-22 21:22:14.655][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-22 21:22:14.656][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-22 21:22:14.658][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-22 21:22:14.659][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-22 21:22:14.660][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-22 21:22:14.661][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-22 21:22:14.663][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-22 21:22:14.664][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-22 21:22:14.665][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-22 21:22:14.666][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-22 21:22:14.668][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-22 21:22:14.669][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-22 21:22:14.670][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-22 21:22:14.671][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-22 21:22:14.672][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-22 21:22:14.674][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-22 21:22:14.675][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-22 21:22:14.676][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-22 21:22:14.677][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-22 21:22:14.679][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-22 21:22:14.680][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-22 21:22:14.681][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-22 21:22:14.682][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-22 21:22:14.684][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-22 21:22:14.685][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-22 21:22:14.686][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-22 21:22:14.688][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-22 21:22:14.689][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-22 21:22:14.690][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-22 21:22:14.691][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-22 21:22:14.693][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-22 21:22:14.694][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-22 21:22:14.695][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-22 21:22:14.696][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-22 21:22:14.697][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-22 21:22:14.699][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-22 21:22:14.700][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-22 21:22:14.701][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-22 21:22:14.702][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-22 21:22:14.704][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-22 21:22:14.705][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-22 21:22:14.706][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-22 21:22:14.707][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-22 21:22:14.709][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-22 21:22:14.710][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-22 21:22:14.711][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-22 21:22:14.712][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-22 21:22:14.714][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-22 21:22:14.715][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-22 21:22:14.716][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-22 21:22:14.717][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-22 21:22:14.719][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-22 21:22:14.720][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-22 21:22:14.721][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-22 21:22:14.722][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-22 21:22:14.724][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-22 21:22:14.725][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-22 21:22:14.726][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-22 21:22:14.727][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-22 21:22:14.729][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-22 21:22:14.730][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-07-22 21:22:14.731][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-22 21:22:14.732][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.733][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:14.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:14.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:14.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:14.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:14.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:14.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:14.754][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:14.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:14.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:14.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:14.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:14.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:14.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:14.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:14.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:14.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.781][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[2024-07-22 21:22:14.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:14.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:14.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.792][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[2024-07-22 21:22:14.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:14.795][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:14.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.798][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[2024-07-22 21:22:14.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:14.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:14.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.804][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[2024-07-22 21:22:14.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:14.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:14.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:14.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:14.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.815][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[2024-07-22 21:22:14.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:14.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:14.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.821][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[2024-07-22 21:22:14.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:14.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:14.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:14.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:14.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-22 21:22:14.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:14.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:14.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.840][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-07-22 21:22:14.841][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-07-22 21:22:14.843][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:14.844][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-22 21:22:14.845][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:14.846][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-22 21:22:14.847][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:14.848][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-22 21:22:14.849][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:14.850][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-07-22 21:22:14.851][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-07-22 21:22:14.852][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-22 21:22:14.852][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:14.853][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-07-22 21:22:14.854][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-22 21:22:14.855][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-07-22 21:22:14.855][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-07-22 21:22:14.855][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-07-22 21:22:14.855][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-07-22 21:22:14.855][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-07-22 21:22:14.855][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-07-22 21:22:14.855][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-07-22 21:22:14.855][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-07-22 21:22:14.855][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-07-22 21:22:14.855][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-07-22 21:22:14.855][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-07-22 21:22:14.856][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-22 21:22:14.857][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-22 21:22:14.857][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-22 21:22:14.857][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-22 21:22:14.858][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-22 21:22:14.859][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:22:14.860][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:22:14.861][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-22 21:22:14.862][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-22 21:22:14.862][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-22 21:22:14.863][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-22 21:22:14.864][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-22 21:22:14.864][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-07-22 21:22:14.865][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-22 21:22:14.866][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-22 21:22:14.867][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-22 21:22:14.868][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-07-22 21:22:14.868][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-07-22 21:22:14.869][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-22 21:22:14.870][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-22 21:22:14.872][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-07-22 21:22:14.873][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-22 21:22:14.875][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-22 21:22:14.876][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-22 21:22:14.879][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-07-22 21:22:14.880][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-07-22 21:22:14.881][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-07-22 21:22:14.883][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-07-22 21:22:14.884][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-22 21:22:14.885][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-22 21:22:14.886][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-07-22 21:22:14.887][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-07-22 21:22:14.888][biodb::testThat]
biodb.INFO [2024-07-22 21:22:14.889][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-07-22 21:22:14.890][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-22 21:22:14.891][biodb::testThat]
biodb.DEBUG[2024-07-22 21:22:14.894][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-07-22 21:22:14.897][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-22 21:22:14.899][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-07-22 21:22:14.900][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-22 21:22:14.902][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-07-22 21:22:14.905][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[2024-07-22 21:22:14.908][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-22 21:22:14.909][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-07-22 21:22:14.910][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-22 21:22:14.912][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-07-22 21:22:14.916][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-07-22 21:22:14.917][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-22 21:22:14.918][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-07-22 21:22:14.919][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-22 21:22:14.920][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-22 21:22:14.922][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-22 21:22:14.923][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-22 21:22:14.924][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-22 21:22:14.924][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-22 21:22:14.927][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:14.928][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:14.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:14.933][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:14.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:14.935][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:14.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-22 21:22:14.937][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-07-22 21:22:14.940][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-22 21:22:14.941][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-22 21:22:14.942][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-07-22 21:22:15.337][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2024-07-22 21:22:16.383][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-22 21:22:16.388][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-07-22 21:22:16.395][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-07-22 21:22:16.400][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-07-22 21:22:16.404][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-22 21:22:16.406][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-22 21:22:16.408][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-22 21:22:16.412][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-22 21:22:16.413][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:16.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:16.423][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:16.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:16.427][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:16.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-22 21:22:16.436][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:16.439][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:16.440][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:16.442][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:16.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:16.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:16.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:16.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:16.453][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:22:16.455][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:22:16.457][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:16.459][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:16.462][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-22 21:22:16.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-22 21:22:16.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:16.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:16.475][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:22:16.479][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:22:16.480][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:16.481][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:16.483][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-22 21:22:16.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-22 21:22:16.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:16.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:16.489][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-22 21:22:16.491][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-22 21:22:16.493][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:16.494][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:16.497][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-22 21:22:16.499][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-22 21:22:16.500][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:16.501][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:16.503][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:22:16.504][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:22:16.505][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:16.506][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:16.508][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:22:16.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-22 21:22:16.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:16.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:16.513][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:22:16.514][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:22:16.515][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:16.516][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:16.518][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-22 21:22:16.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-22 21:22:16.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:16.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:16.523][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:16.525][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:16.526][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:16.527][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:16.529][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:16.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-22 21:22:16.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:16.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:16.535][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:22:16.536][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:22:16.538][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:16.539][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:16.542][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-22 21:22:16.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-22 21:22:16.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:16.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:16.546][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:22:16.547][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:22:16.548][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:16.548][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:16.550][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-22 21:22:16.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-22 21:22:16.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:16.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:16.554][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:22:16.555][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:22:16.556][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:16.557][ef$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:16.559][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-22 21:22:16.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-22 21:22:16.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:16.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:16.563][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:16.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:16.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:16.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:16.567][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:16.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:16.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:16.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:16.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:16.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:16.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:16.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:16.576][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-22 21:22:16.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-22 21:22:16.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:16.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:16.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:16.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:16.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:16.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:16.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:16.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:16.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:16.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:16.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:16.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:16.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:16.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:16.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:16.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:16.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:16.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:16.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:16.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:16.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:16.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-22 21:22:16.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-22 21:22:16.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-22 21:22:16.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-22 21:22:16.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-22 21:22:16.616][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-07-22 21:22:16.621][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-22 21:22:16.624][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-07-22 21:22:16.625][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-07-22 21:22:16.627][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-22 21:22:16.628][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-22 21:22:16.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-22 21:22:16.631][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-22 21:22:16.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-22 21:22:16.633][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-22 21:22:16.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
>
> proc.time()
user system elapsed
24.840 0.684 59.565
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 0.939 | 0.072 | 2.304 | |
| ChebiEntry | 0.163 | 0.000 | 0.164 | |