Pierrick Roger
| Snapshot Date: 2024-06-26 14:00 -0400 (Wed, 26 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: RELEASE_3_19 |
| git_last_commit: fad38a4 |
| git_last_commit_date: 2024-04-30 11:37:31 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-28 17:39 -0400 (Fri, 28 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4760 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4362 |
| 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 200/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.10.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | 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: 1.10.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings biodbChebi_1.10.0.tar.gz |
| StartedAt: 2024-06-26 21:01:19 -0400 (Wed, 26 Jun 2024) |
| EndedAt: 2024-06-26 21:03:30 -0400 (Wed, 26 Jun 2024) |
| EllapsedTime: 131.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbChebi.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings biodbChebi_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 ‘1.10.0’
* 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-3.19-bioc/R/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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 4.4.0 (2024-04-24) -- "Puppy Cup"
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 [2024-06-26 21:02:03.334][biodb::testContext]
biodb.INFO [2024-06-26 21:02:03.336][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-26 21:02:03.337][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-06-26 21:02:03.339][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-26 21:02:03.340][biodb::testContext]
biodb.INFO [2024-06-26 21:02:03.347][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-26 21:02:03.350][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-06-26 21:02:03.365][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-26 21:02:03.369][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-26 21:02:03.370][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-26 21:02:03.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.375][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-26 21:02:03.400][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-26 21:02:03.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.406][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-26 21:02:03.407][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-26 21:02:03.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.411][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-26 21:02:03.412][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-26 21:02:03.413][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-26 21:02:03.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.416][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[2024-06-26 21:02:03.417][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-26 21:02:03.419][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-26 21:02:03.420][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-26 21:02:03.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.424][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-26 21:02:03.425][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-26 21:02:03.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.428][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.DEBUG[2024-06-26 21:02:03.429][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-26 21:02:03.430][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-26 21:02:03.431][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-26 21:02:03.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.435][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-26 21:02:03.437][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-26 21:02:03.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.441][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-26 21:02:03.442][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-26 21:02:03.443][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-26 21:02:03.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.447][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-26 21:02:03.448][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-26 21:02:03.449][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-26 21:02:03.450][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-26 21:02:03.451][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-26 21:02:03.452][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-26 21:02:03.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.456][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-26 21:02:03.457][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-26 21:02:03.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.461][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-26 21:02:03.462][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-26 21:02:03.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.466][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-26 21:02:03.467][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-26 21:02:03.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.471][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-26 21:02:03.472][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-26 21:02:03.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.476][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-26 21:02:03.477][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-26 21:02:03.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.481][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-26 21:02:03.482][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-26 21:02:03.487][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-26 21:02:03.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.491][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-26 21:02:03.492][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-26 21:02:03.493][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-26 21:02:03.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.501][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-26 21:02:03.539][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:03.590][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-26 21:02:03.592][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:03.593][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:02:03.594][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:03.595][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:02:03.596][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:03.597][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 21:02:03.598][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-26 21:02:03.599][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:02:03.600][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:03.601][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-26 21:02:03.602][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:02:03.603][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:03.604][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:03.605][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-26 21:02:03.605][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-26 21:02:03.605][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-26 21:02:03.605][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-26 21:02:03.605][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-26 21:02:03.607][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 21:02:03.608][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:03.609][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:03.610][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:02:03.611][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:03.612][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:03.613][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:02:03.615][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:03.616][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:02:03.617][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:02:03.619][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:03.621][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:03.622][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-26 21:02:03.624][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:03.625][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-26 21:02:03.626][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:03.627][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:02:03.628][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:03.629][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:02:03.630][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:03.631][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 21:02:03.632][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-26 21:02:03.634][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:02:03.635][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:03.636][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-26 21:02:03.637][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:02:03.638][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:03.639][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:03.640][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-26 21:02:03.640][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-26 21:02:03.640][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-26 21:02:03.640][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-26 21:02:03.640][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-26 21:02:03.641][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 21:02:03.642][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:03.643][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:03.644][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:02:03.645][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:03.646][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:03.647][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:02:03.648][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:03.649][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:02:03.650][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:02:03.651][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:03.652][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:03.653][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-26 21:02:03.655][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:03.656][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-26 21:02:03.657][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:03.658][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:02:03.659][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:03.660][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:02:03.661][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:03.662][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 21:02:03.663][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-26 21:02:03.664][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:02:03.665][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:03.666][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-26 21:02:03.667][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:02:03.668][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:03.669][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:03.670][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:03.671][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 21:02:03.672][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:03.673][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:03.674][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:02:03.675][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:03.676][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:03.677][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:02:03.678][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:03.678][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:02:03.679][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:02:03.680][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:03.681][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:03.682][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-26 21:02:03.684][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:03.685][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-26 21:02:03.686][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:03.687][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:02:03.688][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:03.689][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:02:03.690][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:03.691][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 21:02:03.692][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-26 21:02:03.693][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:02:03.693][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:03.694][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-26 21:02:03.695][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:02:03.696][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:03.697][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:03.698][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:03.699][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 21:02:03.700][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:03.701][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:03.702][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:02:03.703][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:03.704][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:03.705][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:02:03.705][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:03.706][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:02:03.707][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:02:03.708][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:03.709][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:03.713][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-26 21:02:03.714][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:03.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:03.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:03.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:03.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:03.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:03.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:03.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:03.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.732][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[2024-06-26 21:02:03.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:03.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:03.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:03.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:03.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.740][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[2024-06-26 21:02:03.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:03.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:03.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:03.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:03.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.748][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[2024-06-26 21:02:03.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:03.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:03.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:03.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:03.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.757][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[2024-06-26 21:02:03.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:03.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:03.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:03.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:03.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.765][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[2024-06-26 21:02:03.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:03.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:03.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.769][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[2024-06-26 21:02:03.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:03.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:03.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.774][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[2024-06-26 21:02:03.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:03.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:03.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:03.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:03.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:03.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:03.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.787][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-26 21:02:03.792][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-26 21:02:03.793][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-26 21:02:03.795][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-26 21:02:03.796][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-26 21:02:03.797][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-26 21:02:03.799][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-26 21:02:03.800][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-26 21:02:03.802][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-26 21:02:03.803][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-26 21:02:03.804][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-26 21:02:03.806][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-26 21:02:03.807][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-26 21:02:03.808][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-26 21:02:03.810][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-26 21:02:03.811][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-26 21:02:03.812][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-26 21:02:03.814][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-26 21:02:03.815][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-26 21:02:03.816][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-26 21:02:03.818][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-26 21:02:03.819][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-26 21:02:03.820][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-26 21:02:03.822][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-26 21:02:03.823][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-26 21:02:03.824][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-26 21:02:03.826][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-26 21:02:03.827][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-26 21:02:03.828][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-26 21:02:03.830][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-26 21:02:03.831][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-26 21:02:03.832][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-26 21:02:03.834][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-26 21:02:03.835][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-26 21:02:03.836][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-26 21:02:03.844][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-26 21:02:03.846][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-26 21:02:03.847][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-26 21:02:03.848][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-26 21:02:03.850][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-26 21:02:03.851][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-26 21:02:03.852][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-26 21:02:03.854][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-26 21:02:03.855][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-26 21:02:03.856][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-26 21:02:03.858][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-26 21:02:03.859][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-26 21:02:03.860][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-26 21:02:03.862][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-26 21:02:03.863][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-26 21:02:03.864][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-26 21:02:03.866][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-26 21:02:03.867][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-26 21:02:03.868][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-26 21:02:03.869][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-26 21:02:03.871][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-26 21:02:03.872][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-26 21:02:03.874][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-26 21:02:03.875][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-26 21:02:03.876][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-26 21:02:03.877][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-26 21:02:03.879][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-26 21:02:03.880][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-26 21:02:03.881][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-26 21:02:03.883][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-26 21:02:03.884][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-26 21:02:03.885][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-26 21:02:03.887][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-26 21:02:03.888][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-26 21:02:03.889][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-26 21:02:03.890][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-26 21:02:03.892][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-26 21:02:03.893][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-26 21:02:03.894][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-26 21:02:03.896][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-26 21:02:03.897][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-26 21:02:03.898][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-26 21:02:03.900][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-26 21:02:03.901][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-26 21:02:03.902][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-26 21:02:03.904][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-26 21:02:03.905][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-26 21:02:03.906][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-26 21:02:03.912][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-26 21:02:03.914][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-26 21:02:03.917][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-26 21:02:03.918][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:03.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:03.920][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:03.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:03.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:03.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:03.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.931][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[2024-06-26 21:02:03.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:03.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:03.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:03.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:03.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:03.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:03.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:03.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:03.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.943][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[2024-06-26 21:02:03.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:03.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:03.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:03.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:03.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:03.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:03.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:03.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:03.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:03.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:03.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:03.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:03.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:03.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:03.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:03.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:03.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:03.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:03.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:03.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:03.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.972][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[2024-06-26 21:02:03.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:03.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:03.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:03.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:03.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:03.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:03.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:03.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:03.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:03.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:03.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:03.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:03.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.990][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[2024-06-26 21:02:03.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:03.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:03.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:03.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:03.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:03.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:03.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:03.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:03.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:04.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:04.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:04.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:04.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:04.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:04.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:04.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:04.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:04.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:04.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:04.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:04.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:04.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:04.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:04.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:04.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:04.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:04.015][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[2024-06-26 21:02:04.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:04.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:04.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:04.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:04.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:04.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:04.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:04.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:04.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:04.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:04.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:04.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:04.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:04.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:04.029][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-06-26 21:02:04.039][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-06-26 21:02:04.040][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:04.041][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-26 21:02:04.042][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:04.043][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:02:04.044][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:04.045][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:02:04.046][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:04.047][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-06-26 21:02:04.048][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-26 21:02:04.049][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:02:04.050][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:04.051][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-06-26 21:02:04.052][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:02:04.053][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-06-26 21:02:04.053][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-06-26 21:02:04.053][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-06-26 21:02:04.053][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-06-26 21:02:04.053][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-06-26 21:02:04.053][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-06-26 21:02:04.053][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-06-26 21:02:04.053][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-06-26 21:02:04.053][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-06-26 21:02:04.053][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-06-26 21:02:04.053][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-06-26 21:02:04.054][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:04.055][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-26 21:02:04.055][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-26 21:02:04.055][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-26 21:02:04.056][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-26 21:02:04.057][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:04.058][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:04.059][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:02:04.060][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:04.061][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:04.062][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:02:04.062][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-26 21:02:04.062][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-06-26 21:02:04.063][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:02:04.064][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:02:04.065][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:04.066][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-06-26 21:02:04.066][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-06-26 21:02:04.072][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-26 21:02:04.074][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-26 21:02:04.076][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-06-26 21:02:04.077][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-26 21:02:04.079][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-26 21:02:04.080][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-26 21:02:04.113][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-06-26 21:02:04.115][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-06-26 21:02:04.119][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-06-26 21:02:04.124][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-06-26 21:02:04.129][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-26 21:02:04.130][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-26 21:02:04.131][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-06-26 21:02:04.132][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-06-26 21:02:04.143][biodb::testThat]
biodb.INFO [2024-06-26 21:02:04.145][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-06-26 21:02:04.146][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:02:04.147][biodb::testThat]
biodb.TRACE[2024-06-26 21:02:04.151][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-06-26 21:02:04.153][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-26 21:02:04.157][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-26 21:02:04.166][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:04.167][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:04.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:04.183][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:04.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:04.186][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:04.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:04.198][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:04.199][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:04.200][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.201][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:04.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:04.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.221][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:04.222][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:04.223][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.224][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.252][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:04.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:04.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.257][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:04.258][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:04.259][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.260][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.262][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:04.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:04.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.266][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:04.267][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:04.268][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.269][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.270][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:04.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:04.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.274][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:04.276][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:04.276][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.277][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.279][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:04.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:04.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.283][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:04.284][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:04.285][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.286][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.287][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:04.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:04.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.292][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:04.293][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:04.294][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.295][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.296][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:04.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:04.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.301][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:04.302][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:04.303][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.304][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.305][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:04.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:04.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.309][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:04.310][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:04.311][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.312][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.314][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:04.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:04.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.318][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:04.319][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:04.320][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.321][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.322][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:04.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:04.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.327][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:04.328][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:04.329][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.330][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.331][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:04.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:04.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.335][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:04.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:04.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.339][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:04.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:04.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:04.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:04.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.348][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:04.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:04.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:04.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:04.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:04.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:04.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:04.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:04.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:04.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:04.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:04.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:04.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:04.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:04.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:04.429][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-06-26 21:02:04.432][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:04.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:04.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.436][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:04.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:04.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.464][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:04.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:04.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.470][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:04.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:04.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.474][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:04.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:04.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.478][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:04.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:04.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.482][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-26 21:02:04.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-26 21:02:04.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.486][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-26 21:02:04.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-26 21:02:04.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.491][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-26 21:02:04.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-26 21:02:04.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.495][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-26 21:02:04.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-26 21:02:04.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:04.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:04.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.537][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:04.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:04.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:04.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:04.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:04.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:04.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:04.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:04.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:04.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:04.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:04.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:04.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:04.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:04.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.574][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:04.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:04.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.578][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:04.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:04.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.582][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:04.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:04.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:04.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:04.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:04.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:04.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:04.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:04.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.607][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:04.608][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:04.609][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.610][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:04.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:04.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.623][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:04.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:04.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.664][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:04.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:04.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.669][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:04.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:04.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.673][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:04.674][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:04.675][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.676][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.677][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:04.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:04.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.689][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:04.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:04.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.694][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:04.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:04.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.698][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:04.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:04.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.702][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:04.703][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:04.704][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.705][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.706][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:04.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:04.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.718][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:04.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:04.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.723][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:04.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:04.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.727][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:04.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:04.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.731][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:04.732][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:04.733][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.734][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.735][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:04.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:04.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.747][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:04.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:04.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.751][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:04.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:04.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.755][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:04.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:04.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.759][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:04.760][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:04.761][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.762][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.763][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:04.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:04.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.775][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:04.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:04.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.779][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:04.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:04.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.784][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:04.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:04.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.788][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:04.789][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:04.790][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.791][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.792][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:04.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:04.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.803][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:04.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:04.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.808][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:04.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:04.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.812][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:04.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:04.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.816][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:04.817][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:04.818][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.819][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.820][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:04.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:04.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.832][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-26 21:02:04.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:04.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.836][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-26 21:02:04.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:04.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.840][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-26 21:02:04.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:04.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.844][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-26 21:02:04.845][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:04.846][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.847][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.848][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-26 21:02:04.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:04.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.860][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:04.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:04.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.865][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:04.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:04.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.869][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:04.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:04.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.873][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:04.874][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:04.875][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.876][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.877][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:04.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:04.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.889][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:04.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:04.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.893][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:04.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:04.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.903][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:04.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:04.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.908][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:04.909][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:04.910][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.910][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.912][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:04.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:04.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.924][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:04.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:04.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.928][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:04.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:04.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.932][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:04.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:04.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.937][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:04.938][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:04.939][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.940][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.941][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:04.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:04.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.953][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:04.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:04.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.958][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:04.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:04.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.962][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:04.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:04.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.966][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:04.967][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:04.968][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.970][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.971][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:04.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:04.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.983][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:04.985][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:04.986][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.987][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:04.992][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:04.993][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:04.994][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:04.995][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.000][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:05.001][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:05.002][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.003][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.008][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:05.009][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:05.010][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.011][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.016][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:05.017][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:05.018][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.019][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.024][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:05.026][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:05.027][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.028][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.032][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:05.034][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:05.035][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.036][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.041][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:05.042][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:05.043][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.044][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.050][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-26 21:02:05.051][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:05.053][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.054][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.061][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:05.063][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:05.065][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.066][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.073][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:05.075][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:05.077][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.078][ef$get] fields variable is a list.
biodb.INFO [2024-06-26 21:02:05.090][biodb::testThat]
biodb.INFO [2024-06-26 21:02:05.092][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-26 21:02:05.094][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:02:05.096][biodb::testThat]
biodb.DEBUG[2024-06-26 21:02:05.112][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-06-26 21:02:05.120][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-26 21:02:05.126][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-06-26 21:02:05.128][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 21:02:05.129][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-06-26 21:02:05.131][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 21:02:05.155][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-26 21:02:05.157][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-26 21:02:05.167][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:05.168][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:05.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:05.174][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:05.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:05.176][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:05.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:05.180][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:05.181][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:05.182][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.183][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:05.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:05.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.206][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:05.208][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:05.209][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.210][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.211][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:05.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:05.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.216][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:05.217][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:05.218][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.219][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.220][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:05.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:05.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.224][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:05.225][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:05.226][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.227][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.229][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:05.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:05.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.233][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:05.234][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:05.235][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.236][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.238][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:05.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:05.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.242][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:05.243][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:05.244][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.245][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.246][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:05.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:05.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.250][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:05.252][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:05.252][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.253][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.255][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:05.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:05.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.259][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:05.260][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:05.261][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.262][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.263][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:05.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:05.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.267][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:05.268][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:05.269][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.270][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.272][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:05.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:05.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.276][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:05.277][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:05.278][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.279][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.280][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:05.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:05.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.285][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:05.286][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:05.287][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.287][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.289][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:05.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:05.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.293][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:05.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:05.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.297][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:05.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:05.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:05.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:05.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.305][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:05.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:05.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:05.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:05.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:05.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:05.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:05.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:05.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:05.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:05.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:05.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:05.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:05.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:05.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:05.333][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-06-26 21:02:05.334][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-26 21:02:05.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-26 21:02:05.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.338][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-26 21:02:05.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-26 21:02:05.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.342][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-26 21:02:05.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-26 21:02:05.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-26 21:02:05.353][biodb::testThat]
biodb.INFO [2024-06-26 21:02:05.354][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-26 21:02:05.355][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:02:05.356][biodb::testThat]
biodb.TRACE[2024-06-26 21:02:05.359][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:05.360][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:05.361][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.362][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:05.364][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-06-26 21:02:05.395][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:05.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:05.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.399][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:05.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:05.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:05.403][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:05.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:05.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:05.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:05.410][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-06-26 21:02:05.416][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-06-26 21:02:05.437][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-26 21:02:05.454][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-06-26 21:02:05.455][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 21:02:05.457][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-06-26 21:02:05.480][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[2024-06-26 21:02:05.484][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:05.485][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:05.487][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-26 21:02:06.694][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-26 21:02:07.533][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:07.537][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-06-26 21:02:07.561][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-06-26 21:02:07.565][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-06-26 21:02:07.581][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:07.583][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:07.585][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:07.586][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:07.588][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:07.589][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:07.590][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:07.592][ef$get] fields variable is a list.
biodb.INFO [2024-06-26 21:02:07.598][biodb::testThat]
biodb.INFO [2024-06-26 21:02:07.599][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-06-26 21:02:07.601][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:02:07.602][biodb::testThat]
biodb.TRACE[2024-06-26 21:02:07.639][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:07.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:07.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:07.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:07.643][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:07.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:07.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:07.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:07.647][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:07.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:07.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:07.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:07.702][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-26 21:02:07.705][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-26 21:02:07.706][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-26 21:02:07.707][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 21:02:07.708][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-06-26 21:02:07.721][biodb::testThat]
biodb.INFO [2024-06-26 21:02:07.722][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-06-26 21:02:07.723][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:02:07.724][biodb::testThat]
biodb.TRACE[2024-06-26 21:02:07.748][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:07.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:07.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:07.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:07.752][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:07.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:07.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:07.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:07.756][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:07.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:07.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:07.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:07.760][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:07.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:07.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:07.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:07.764][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:07.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:07.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:07.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:07.767][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:07.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:07.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:07.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:07.771][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-26 21:02:07.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-26 21:02:07.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:07.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:07.775][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-26 21:02:07.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-26 21:02:07.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:07.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:07.779][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-26 21:02:07.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-26 21:02:07.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:07.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:07.782][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-26 21:02:07.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-26 21:02:07.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:07.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:07.802][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:07.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:07.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:07.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:07.806][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:07.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:07.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:07.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:07.810][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:07.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:07.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:07.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:07.814][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:07.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:07.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:07.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:07.817][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:07.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:07.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:07.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:07.821][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:07.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:07.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:07.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:07.825][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-26 21:02:07.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-26 21:02:07.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:07.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:07.828][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-26 21:02:07.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-26 21:02:07.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:07.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:07.832][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-26 21:02:07.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-26 21:02:07.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:07.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:07.836][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-26 21:02:07.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-26 21:02:07.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:07.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-26 21:02:07.844][biodb::testThat]
biodb.INFO [2024-06-26 21:02:07.845][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-26 21:02:07.846][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:02:07.847][biodb::testThat]
biodb.INFO [2024-06-26 21:02:07.854][biodb::testThat]
biodb.INFO [2024-06-26 21:02:07.855][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-26 21:02:07.856][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:02:07.857][biodb::testThat]
biodb.INFO [2024-06-26 21:02:07.864][biodb::testThat]
biodb.INFO [2024-06-26 21:02:07.865][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-26 21:02:07.866][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:02:07.867][biodb::testThat]
biodb.DEBUG[2024-06-26 21:02:07.870][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-06-26 21:02:08.412][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-06-26 21:02:09.745][biodb::testThat]
biodb.INFO [2024-06-26 21:02:09.747][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-26 21:02:09.749][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:02:09.751][biodb::testThat]
biodb.DEBUG[2024-06-26 21:02:10.191][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[2024-06-26 21:02:10.650][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:10.652][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:10.654][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:10.656][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:10.658][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:10.660][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:10.661][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:10.663][ef$get] fields variable is a list.
biodb.INFO [2024-06-26 21:02:10.667][biodb::testThat]
biodb.INFO [2024-06-26 21:02:10.669][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2024-06-26 21:02:10.671][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:02:10.673][biodb::testThat]
biodb.TRACE[2024-06-26 21:02:10.717][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:10.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:10.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:10.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:10.722][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:10.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:10.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:10.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:10.726][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:10.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:10.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:10.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:10.818][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-26 21:02:10.822][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-26 21:02:10.824][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-26 21:02:10.825][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 21:02:10.827][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-26 21:02:10.892][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-26 21:02:10.896][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-26 21:02:10.897][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-26 21:02:10.898][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 21:02:10.900][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-06-26 21:02:10.920][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-26 21:02:10.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-26 21:02:10.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:10.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:10.928][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:10.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:10.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:10.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:10.932][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:10.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:10.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:10.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:10.936][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:10.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:10.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:10.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:10.940][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:10.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:10.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:10.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:10.944][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:10.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:10.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:10.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:10.956][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-26 21:02:10.973][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:10.974][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:10.990][private$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[2024-06-26 21:02:11.377][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[2024-06-26 21:02:11.778][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:11.780][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-06-26 21:02:11.784][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-06-26 21:02:11.787][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:11.788][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:11.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:11.793][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:11.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:11.795][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:11.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:11.797][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-06-26 21:02:11.840][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-26 21:02:11.842][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-06-26 21:02:11.843][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-26 21:02:11.844][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-26 21:02:11.845][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 21:02:11.846][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-26 21:02:11.847][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-26 21:02:11.848][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-26 21:02:11.858][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:11.859][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:11.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:11.864][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:11.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:11.866][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:11.867][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.DEBUG[2024-06-26 21:02:11.868][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-06-26 21:02:11.870][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:11.871][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:11.872][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-06-26 21:02:12.314][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-06-26 21:02:12.750][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:12.753][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-06-26 21:02:12.758][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-06-26 21:02:12.762][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-06-26 21:02:12.764][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-26 21:02:12.765][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-26 21:02:12.767][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-26 21:02:12.769][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:12.770][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:12.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:12.778][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:12.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:12.781][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:12.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:12.785][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:12.787][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:12.788][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:12.789][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:12.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:12.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:12.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:12.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:12.797][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:12.799][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:12.800][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:12.802][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:12.804][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:12.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:12.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:12.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:12.810][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:12.811][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:12.813][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:12.814][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:12.817][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:12.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:12.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:12.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:12.823][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:12.824][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:12.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:12.827][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:12.829][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:12.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:12.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:12.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:12.835][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:12.836][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:12.838][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:12.839][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:12.841][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:12.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:12.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:12.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:12.847][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:12.849][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:12.850][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:12.851][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:12.853][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:12.855][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:12.856][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:12.858][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:12.859][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:12.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:12.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:12.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:12.865][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:12.867][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:12.868][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:12.870][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:12.872][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:12.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:12.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:12.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:12.878][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:12.879][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:12.880][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:12.882][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:12.883][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:12.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:12.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:12.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:12.888][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:12.889][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:12.890][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:12.891][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:12.892][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:12.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:12.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:12.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:12.896][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:12.897][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:12.898][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:12.899][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:12.900][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:12.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:12.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:12.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:12.904][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:12.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:12.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:12.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:12.907][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:12.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:12.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:12.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:12.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:12.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:12.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:12.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:12.915][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:12.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:12.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:12.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:12.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:12.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:12.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:12.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:12.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:12.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:12.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:12.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:12.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:12.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:12.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:12.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:12.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:12.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:12.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:12.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:12.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:12.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:12.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:12.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:12.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:12.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:12.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:12.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:12.940][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-06-26 21:02:12.956][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:12.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:12.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:12.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:12.960][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:12.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:12.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:12.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:12.964][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:12.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:12.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:12.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:12.969][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[2024-06-26 21:02:12.972][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:12.972][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:12.974][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-26 21:02:13.360][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-26 21:02:13.799][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:13.802][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-06-26 21:02:13.807][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-06-26 21:02:13.831][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:13.833][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:13.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:13.840][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:13.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:13.843][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:13.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:13.846][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:13.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:13.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:13.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:13.851][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:13.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:13.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:13.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:13.857][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:13.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:13.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:13.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:13.862][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:13.863][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:13.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:13.878][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:13.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:13.882][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:13.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:13.885][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-06-26 21:02:13.887][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-26 21:02:13.890][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-06-26 21:02:13.892][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-26 21:02:13.893][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-26 21:02:13.895][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 21:02:13.897][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-26 21:02:13.898][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-26 21:02:13.900][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-26 21:02:13.925][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:13.927][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:13.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:13.936][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:13.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:13.939][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:13.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:13.942][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-06-26 21:02:13.945][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:13.946][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:13.947][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-06-26 21:02:14.352][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-06-26 21:02:14.810][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:14.813][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-06-26 21:02:14.818][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-06-26 21:02:14.822][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-06-26 21:02:14.824][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-26 21:02:14.826][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-26 21:02:14.828][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-26 21:02:14.831][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:14.832][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:14.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:14.841][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:14.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:14.843][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:14.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:14.849][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:14.851][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:14.852][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:14.853][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:14.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:14.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:14.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:14.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:14.862][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:14.864][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:14.865][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:14.867][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:14.869][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:14.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:14.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:14.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:14.875][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:14.877][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:14.878][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:14.892][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:14.899][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:14.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:14.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:14.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:14.903][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:14.904][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:14.905][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:14.906][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:14.908][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:14.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:14.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:14.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:14.912][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:14.913][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:14.914][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:14.915][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:14.916][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:14.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:14.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:14.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:14.921][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:14.922][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:14.923][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:14.924][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:14.925][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:14.926][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:14.927][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:14.928][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:14.929][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:14.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:14.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:14.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:14.934][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:14.935][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:14.936][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:14.937][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:14.938][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:14.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:14.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:14.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:14.942][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:14.943][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:14.944][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:14.945][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:14.947][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:14.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:14.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:14.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:14.951][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:14.952][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:14.953][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:14.954][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:14.955][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:14.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:14.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:14.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:14.959][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:14.960][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:14.961][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:14.962][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:14.963][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:14.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:14.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:14.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:14.968][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:14.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:14.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:14.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:14.972][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:14.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:14.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:14.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:14.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:14.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:14.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:14.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:14.980][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:14.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:14.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:14.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:14.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:14.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:14.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:14.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:14.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:14.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:14.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:14.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:14.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:14.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:14.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:14.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:14.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:14.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:14.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:14.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:14.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:15.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:15.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:15.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:15.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:15.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:15.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:15.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:15.007][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-06-26 21:02:15.008][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:15.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:15.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:15.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:15.012][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:15.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:15.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:15.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:15.016][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:15.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:15.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:15.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:15.036][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-26 21:02:15.039][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-26 21:02:15.040][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-26 21:02:15.041][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 21:02:15.042][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-26 21:02:15.046][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:15.046][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:15.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:15.051][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:15.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:15.053][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:15.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:15.055][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:15.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:15.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:15.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:15.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:15.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:15.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:15.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:15.063][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:15.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:15.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:15.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:15.067][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:15.068][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:15.068][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:15.077][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:15.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:15.079][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:15.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:15.081][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-06-26 21:02:15.082][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-26 21:02:15.083][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-06-26 21:02:15.085][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-26 21:02:15.086][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-26 21:02:15.087][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 21:02:15.088][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-26 21:02:15.089][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-26 21:02:15.090][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-26 21:02:15.092][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:15.093][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:15.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:15.098][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:15.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:15.100][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:15.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:15.102][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-06-26 21:02:15.105][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:15.106][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:15.107][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-06-26 21:02:15.505][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-06-26 21:02:15.905][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:15.908][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-06-26 21:02:15.911][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-06-26 21:02:15.914][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-06-26 21:02:15.915][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-26 21:02:15.916][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-26 21:02:15.918][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-26 21:02:15.919][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:15.920][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:15.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:15.926][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:15.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:15.928][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:15.928][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[2024-06-26 21:02:15.931][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:15.932][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:15.933][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:15.934][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:15.935][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:15.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:15.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:15.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:15.939][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:15.940][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:15.941][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:15.942][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:15.943][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:15.944][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:15.945][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:15.946][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:15.947][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:15.948][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:15.949][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:15.950][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:15.951][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:15.952][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:15.953][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:15.954][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:15.955][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:15.956][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:15.957][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:15.958][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:15.959][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:15.960][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:15.961][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:15.962][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:15.963][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:15.964][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:15.965][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:15.966][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:15.967][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:15.968][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:15.969][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:15.970][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:15.971][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:15.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:15.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:15.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:15.975][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:15.976][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:15.977][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:15.977][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:15.979][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:15.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:15.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:15.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:15.983][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:15.984][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:15.984][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:15.985][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:15.987][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:15.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:15.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:15.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:15.990][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:15.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:15.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:15.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:15.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:15.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:15.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:15.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:15.998][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:15.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:15.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:16.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:16.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:16.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:16.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:16.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:16.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:16.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:16.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:16.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:16.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:16.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:16.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:16.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:16.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:16.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:16.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:16.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:16.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:16.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:16.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:16.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:16.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:16.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:16.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:16.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:16.024][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-06-26 21:02:16.025][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:16.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:16.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:16.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:16.028][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:16.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:16.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:16.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:16.032][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:16.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:16.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:16.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:16.036][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:16.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:16.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:16.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:16.040][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:16.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:16.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:16.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:16.052][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:16.053][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:16.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:16.058][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:16.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:16.059][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:16.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:16.061][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-06-26 21:02:16.062][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-26 21:02:16.064][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-06-26 21:02:16.065][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-26 21:02:16.066][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-26 21:02:16.067][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 21:02:16.068][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-26 21:02:16.069][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-26 21:02:16.070][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-26 21:02:16.072][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:16.073][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:16.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:16.078][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:16.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:16.080][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:16.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:16.082][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-06-26 21:02:16.084][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:16.085][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:16.087][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-06-26 21:02:16.473][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-06-26 21:02:16.901][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:16.905][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-06-26 21:02:16.913][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-06-26 21:02:16.918][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-06-26 21:02:16.922][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-26 21:02:16.924][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-26 21:02:16.927][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-26 21:02:16.931][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:16.933][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:16.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:16.944][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:16.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:16.947][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:16.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:16.953][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:16.955][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:16.956][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:16.958][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:16.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:16.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:16.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:16.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:16.966][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:16.967][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:16.968][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:16.970][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:16.971][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:16.973][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:16.974][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:16.975][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:16.977][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:16.978][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:16.979][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:16.980][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:16.981][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:16.982][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:16.983][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:16.984][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:16.986][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:16.987][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:16.988][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:16.989][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:16.990][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:16.991][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:16.992][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:16.993][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:16.994][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:16.996][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:16.997][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:16.998][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:16.999][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:17.000][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:17.001][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:17.002][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:17.004][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:17.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:17.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:17.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:17.008][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:17.009][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:17.009][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:17.010][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:17.011][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:17.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:17.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:17.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:17.015][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:17.016][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:17.017][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:17.018][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:17.019][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:17.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:17.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:17.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:17.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:17.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:17.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:17.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:17.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:17.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:17.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:17.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:17.031][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:17.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:17.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:17.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:17.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:17.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:17.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:17.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:17.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:17.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:17.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:17.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:17.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:17.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:17.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:17.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:17.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:17.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:17.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:17.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:17.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:17.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:17.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:17.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:17.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:17.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:17.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:17.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:17.058][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-06-26 21:02:17.060][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:17.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:17.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:17.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:17.063][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:17.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:17.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:17.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:17.078][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:17.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:17.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:17.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:17.082][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:17.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:17.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:17.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:17.086][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:17.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:17.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:17.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:17.089][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:17.090][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:17.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:17.096][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:17.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:17.097][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:17.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:17.100][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-06-26 21:02:17.100][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-26 21:02:17.102][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-06-26 21:02:17.103][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-26 21:02:17.104][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-26 21:02:17.106][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 21:02:17.107][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-26 21:02:17.107][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-26 21:02:17.108][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-26 21:02:17.111][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:17.112][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:17.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:17.117][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:17.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:17.119][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:17.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:17.121][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-06-26 21:02:17.123][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:17.124][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:17.125][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-06-26 21:02:17.510][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-06-26 21:02:17.929][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:17.933][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-06-26 21:02:17.941][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-06-26 21:02:17.946][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-06-26 21:02:17.950][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-26 21:02:17.952][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-26 21:02:17.955][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-26 21:02:17.958][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:17.960][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:17.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:17.972][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:17.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:17.975][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:17.977][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.TRACE[2024-06-26 21:02:17.981][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:17.983][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:17.984][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:17.986][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:17.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:17.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:17.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:17.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:17.994][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:17.995][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:17.997][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:17.998][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:17.999][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:18.001][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:18.002][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:18.003][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:18.005][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:18.006][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:18.007][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:18.008][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:18.010][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:18.011][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:18.012][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:18.013][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:18.014][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:18.015][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:18.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:18.017][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:18.019][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:18.020][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:18.021][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:18.022][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:18.023][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:18.024][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:18.025][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:18.026][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:18.027][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:18.028][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:18.029][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:18.030][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:18.031][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:18.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:18.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:18.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:18.035][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:18.036][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:18.037][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:18.038][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:18.039][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:18.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:18.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:18.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:18.043][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:18.044][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:18.045][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:18.046][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:18.047][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:18.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:18.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:18.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:18.051][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:18.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:18.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:18.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:18.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:18.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:18.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:18.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:18.058][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:18.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:18.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:18.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:18.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:18.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:18.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:18.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:18.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:18.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:18.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:18.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:18.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:18.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:18.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:18.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:18.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:18.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:18.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:18.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:18.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:18.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:18.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:18.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:18.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:18.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:18.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:18.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:18.092][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-06-26 21:02:18.093][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:18.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:18.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:18.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:18.097][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:18.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:18.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:18.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:18.101][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:18.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:18.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:18.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:18.104][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:18.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:18.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:18.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:18.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:18.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:18.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:18.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:18.112][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:18.113][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:18.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:18.118][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:18.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:18.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:18.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:18.122][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-06-26 21:02:18.123][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-26 21:02:18.124][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-06-26 21:02:18.125][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-26 21:02:18.126][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-26 21:02:18.127][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 21:02:18.128][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-26 21:02:18.129][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-26 21:02:18.130][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-26 21:02:18.133][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:18.134][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:18.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:18.143][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:18.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:18.146][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:18.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:18.148][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-06-26 21:02:18.152][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:18.153][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:18.155][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-06-26 21:02:18.548][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-06-26 21:02:19.034][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:19.038][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-06-26 21:02:19.043][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-06-26 21:02:19.047][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-06-26 21:02:19.050][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-26 21:02:19.052][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-26 21:02:19.054][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-26 21:02:19.056][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:19.058][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:19.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:19.067][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:19.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:19.070][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:19.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:19.076][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:19.078][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:19.079][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.081][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:19.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:19.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:19.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:19.090][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:19.091][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:19.093][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.094][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:19.096][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:19.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:19.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:19.103][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:19.104][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:19.106][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.107][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:19.110][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:19.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:19.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:19.117][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:19.118][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:19.120][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.121][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:19.123][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:19.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:19.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:19.129][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:19.131][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:19.132][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.134][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:19.136][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:19.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:19.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:19.143][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:19.144][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:19.146][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.147][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:19.149][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:19.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:19.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:19.156][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:19.157][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:19.159][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.160][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:19.162][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:19.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:19.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:19.167][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:19.168][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:19.169][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.170][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:19.171][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:19.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:19.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:19.175][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:19.176][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:19.177][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.178][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:19.180][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:19.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:19.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:19.184][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:19.185][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:19.186][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.187][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:19.188][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:19.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:19.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:19.192][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:19.193][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:19.206][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.210][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:19.211][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:19.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:19.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:19.215][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:19.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:19.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:19.219][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:19.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:19.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:19.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:19.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:19.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:19.228][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:19.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:19.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:19.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:19.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:19.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:19.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:19.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:19.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:19.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:19.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:19.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:19.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:19.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:19.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:19.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:19.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:19.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:19.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:19.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:19.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:19.256][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-06-26 21:02:19.257][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:19.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:19.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:19.261][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:19.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:19.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:19.264][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:19.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:19.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:19.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:19.268][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:19.269][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:19.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:19.274][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:19.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:19.276][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:19.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:19.278][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-06-26 21:02:19.279][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-26 21:02:19.280][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-06-26 21:02:19.281][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-26 21:02:19.282][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-26 21:02:19.283][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 21:02:19.284][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-26 21:02:19.285][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-26 21:02:19.286][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-26 21:02:19.289][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:19.289][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:19.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:19.294][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:19.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:19.296][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:19.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:19.298][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-06-26 21:02:19.301][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:19.301][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:19.303][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-06-26 21:02:19.698][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-06-26 21:02:20.132][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:20.137][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-06-26 21:02:20.144][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-06-26 21:02:20.150][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-06-26 21:02:20.154][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-26 21:02:20.157][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-26 21:02:20.160][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-26 21:02:20.164][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:20.166][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:20.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:20.179][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:20.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:20.182][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:20.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:20.187][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:20.189][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:20.191][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.192][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:20.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:20.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:20.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:20.199][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:20.201][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:20.202][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.203][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:20.205][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:20.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:20.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:20.209][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:20.211][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:20.212][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.213][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:20.214][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:20.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:20.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:20.219][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:20.220][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:20.221][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.222][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:20.223][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:20.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:20.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:20.227][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:20.228][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:20.229][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.230][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:20.231][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:20.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:20.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:20.235][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:20.236][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:20.237][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.238][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:20.239][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:20.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:20.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:20.243][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:20.252][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:20.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.254][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:20.255][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:20.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:20.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:20.259][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:20.260][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:20.261][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.262][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:20.263][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:20.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:20.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:20.268][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:20.269][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:20.270][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.271][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:20.272][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:20.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:20.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:20.277][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:20.277][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:20.278][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.279][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:20.280][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:20.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:20.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:20.285][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:20.286][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:20.287][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.288][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:20.289][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:20.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:20.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:20.293][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:20.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:20.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:20.297][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:20.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:20.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:20.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:20.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:20.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:20.305][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:20.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:20.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:20.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:20.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:20.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:20.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:20.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:20.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:20.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:20.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:20.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:20.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:20.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:20.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:20.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:20.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:20.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:20.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:20.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:20.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:20.333][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-06-26 21:02:20.334][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:20.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:20.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:20.338][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:20.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:20.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:20.342][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:20.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:20.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:20.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:20.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:20.346][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:20.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:20.351][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:20.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:20.353][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:20.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:20.355][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-06-26 21:02:20.356][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-26 21:02:20.358][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-06-26 21:02:20.359][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-26 21:02:20.360][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-26 21:02:20.361][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 21:02:20.362][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-26 21:02:20.363][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-26 21:02:20.364][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-26 21:02:20.366][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:20.367][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:20.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:20.373][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:20.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:20.374][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:20.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:20.376][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-06-26 21:02:20.379][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:20.380][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:20.381][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-06-26 21:02:20.793][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-06-26 21:02:21.185][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:21.189][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-06-26 21:02:21.196][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-06-26 21:02:21.202][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-06-26 21:02:21.205][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-26 21:02:21.208][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-26 21:02:21.210][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-26 21:02:21.214][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:21.216][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:21.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:21.227][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:21.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:21.230][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:21.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:21.235][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:21.237][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:21.239][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:21.240][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:21.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:21.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:21.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:21.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:21.248][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:21.249][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:21.251][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:21.252][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:21.254][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:21.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:21.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:21.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:21.267][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:21.268][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:21.269][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:21.270][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:21.272][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:21.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:21.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:21.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:21.276][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:21.277][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:21.278][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:21.279][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:21.280][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:21.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:21.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:21.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:21.284][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:21.285][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:21.286][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:21.287][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:21.288][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:21.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:21.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:21.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:21.292][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:21.293][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:21.293][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:21.294][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:21.295][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:21.296][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:21.297][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:21.298][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:21.299][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:21.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:21.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:21.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:21.303][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:21.304][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:21.305][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:21.306][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:21.307][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:21.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:21.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:21.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:21.311][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:21.312][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:21.313][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:21.314][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:21.315][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:21.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:21.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:21.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:21.319][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:21.320][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:21.321][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:21.322][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:21.323][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:21.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:21.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:21.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:21.327][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:21.328][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:21.329][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:21.330][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:21.331][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:21.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:21.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:21.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:21.335][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:21.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:21.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:21.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:21.339][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:21.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:21.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:21.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:21.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:21.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:21.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:21.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:21.346][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:21.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:21.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:21.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:21.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:21.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:21.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:21.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:21.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:21.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:21.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:21.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:21.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:21.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:21.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:21.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:21.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:21.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:21.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:21.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:21.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:21.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:21.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:21.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:21.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:21.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:21.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:21.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:21.373][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-06-26 21:02:21.374][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:21.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:21.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:21.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:21.378][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:21.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:21.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:21.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:21.381][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:21.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:21.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:21.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:21.385][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:21.386][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:21.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:21.391][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:21.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:21.393][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:21.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:21.395][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-06-26 21:02:21.396][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-26 21:02:21.397][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-06-26 21:02:21.398][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-26 21:02:21.399][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-26 21:02:21.400][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 21:02:21.401][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-26 21:02:21.402][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-26 21:02:21.403][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-26 21:02:21.406][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:21.407][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:21.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:21.412][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:21.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:21.414][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:21.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:21.416][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-06-26 21:02:21.418][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:21.419][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:21.421][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-06-26 21:02:22.023][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-06-26 21:02:22.458][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:22.461][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-06-26 21:02:22.467][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-06-26 21:02:22.484][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-06-26 21:02:22.486][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-26 21:02:22.488][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-26 21:02:22.490][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-26 21:02:22.493][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:22.495][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:22.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:22.504][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:22.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:22.506][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:22.508][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[2024-06-26 21:02:22.511][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:22.513][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:22.514][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:22.515][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:22.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:22.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:22.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:22.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:22.522][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:22.524][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:22.525][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:22.526][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:22.527][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:22.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:22.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:22.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:22.532][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:22.533][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:22.534][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:22.535][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:22.536][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:22.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:22.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:22.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:22.540][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:22.542][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:22.542][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:22.543][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:22.545][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:22.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:22.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:22.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:22.548][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:22.549][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:22.550][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:22.551][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:22.552][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:22.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:22.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:22.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:22.556][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:22.557][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:22.558][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:22.559][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:22.560][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:22.561][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:22.562][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:22.563][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:22.564][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:22.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:22.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:22.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:22.568][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:22.569][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:22.570][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:22.571][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:22.572][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:22.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:22.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:22.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:22.576][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:22.577][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:22.578][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:22.579][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:22.580][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:22.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:22.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:22.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:22.584][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:22.585][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:22.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:22.587][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:22.588][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:22.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:22.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:22.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:22.592][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:22.593][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:22.594][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:22.595][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:22.596][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:22.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:22.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:22.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:22.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:22.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:22.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:22.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:22.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:22.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:22.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:22.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:22.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:22.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:22.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:22.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:22.611][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:22.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:22.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:22.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:22.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:22.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:22.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:22.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:22.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:22.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:22.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:22.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:22.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:22.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:22.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:22.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:22.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:22.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:22.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:22.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:22.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:22.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:22.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:22.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:22.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:22.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:22.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:22.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:22.638][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-06-26 21:02:22.639][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:22.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:22.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:22.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:22.643][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:22.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:22.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:22.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:22.647][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:22.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:22.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:22.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:22.651][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:22.651][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:22.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:22.656][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:22.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:22.658][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:22.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:22.660][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-06-26 21:02:22.661][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-26 21:02:22.663][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-06-26 21:02:22.664][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-26 21:02:22.669][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-26 21:02:22.671][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 21:02:22.672][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-26 21:02:22.673][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-26 21:02:22.674][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-26 21:02:22.676][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:22.677][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:22.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:22.682][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:22.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:22.684][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:22.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:22.686][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-06-26 21:02:22.689][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:22.689][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:22.691][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-06-26 21:02:23.081][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-06-26 21:02:23.514][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:23.516][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-06-26 21:02:23.519][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-06-26 21:02:23.521][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-06-26 21:02:23.523][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-26 21:02:23.524][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-26 21:02:23.525][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-26 21:02:23.527][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:23.527][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:23.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:23.533][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:23.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:23.534][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:23.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:23.537][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:23.538][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:23.539][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:23.540][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:23.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:23.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:23.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:23.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:23.546][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:23.547][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:23.549][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:23.550][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:23.552][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:23.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:23.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:23.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:23.558][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:23.560][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:23.561][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:23.563][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:23.565][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:23.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:23.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:23.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:23.571][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:23.572][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:23.574][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:23.575][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:23.577][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:23.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:23.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:23.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:23.582][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:23.590][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:23.591][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:23.593][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:23.595][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:23.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:23.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:23.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:23.602][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:23.603][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:23.605][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:23.606][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:23.608][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:23.610][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:23.612][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:23.613][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:23.615][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:23.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:23.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:23.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:23.622][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:23.624][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:23.625][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:23.627][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:23.629][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:23.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:23.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:23.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:23.636][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:23.637][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:23.639][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:23.641][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:23.643][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:23.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:23.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:23.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:23.649][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:23.651][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:23.653][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:23.654][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:23.656][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:23.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:23.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:23.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:23.663][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:23.665][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:23.667][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:23.668][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:23.670][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:23.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:23.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:23.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:23.677][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:23.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:23.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:23.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:23.683][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:23.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:23.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:23.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:23.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:23.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:23.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:23.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:23.699][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:23.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:23.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:23.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:23.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:23.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:23.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:23.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:23.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:23.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:23.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:23.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:23.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:23.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:23.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:23.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:23.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:23.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:23.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:23.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:23.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:23.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:23.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:23.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:23.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:23.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:23.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:23.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:23.769][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-06-26 21:02:23.771][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:23.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:23.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:23.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:23.775][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:23.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:23.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:23.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:23.782][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:23.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:23.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:23.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:23.788][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:23.789][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:23.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:23.797][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:23.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:23.799][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:23.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:23.802][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-06-26 21:02:23.803][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-26 21:02:23.805][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-06-26 21:02:23.807][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-26 21:02:23.808][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-26 21:02:23.809][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 21:02:23.810][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-26 21:02:23.812][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-26 21:02:23.812][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-26 21:02:23.815][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:23.816][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:23.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:23.823][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:23.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:23.826][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:23.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:23.831][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-06-26 21:02:23.837][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:23.843][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:23.846][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-06-26 21:02:24.296][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-06-26 21:02:24.706][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:24.709][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-06-26 21:02:24.715][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-06-26 21:02:24.719][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-06-26 21:02:24.721][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-26 21:02:24.723][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-26 21:02:24.725][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-26 21:02:24.728][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:24.729][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:24.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:24.739][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:24.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:24.742][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:24.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:24.747][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:24.749][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:24.751][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:24.752][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:24.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:24.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:24.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:24.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:24.762][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:24.764][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:24.765][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:24.767][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:24.769][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:24.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:24.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:24.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:24.777][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:24.779][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:24.781][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:24.782][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:24.784][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:24.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:24.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:24.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:24.792][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:24.794][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:24.796][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:24.797][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:24.800][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:24.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:24.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:24.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:24.806][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:24.807][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:24.809][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:24.810][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:24.812][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:24.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:24.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:24.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:24.818][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:24.819][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:24.820][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:24.821][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:24.822][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:24.823][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:24.824][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:24.825][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:24.826][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:24.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:24.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:24.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:24.830][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:24.831][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:24.832][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:24.833][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:24.834][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:24.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:24.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:24.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:24.838][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:24.839][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:24.840][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:24.841][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:24.842][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:24.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:24.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:24.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:24.846][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:24.847][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:24.848][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:24.849][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:24.850][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:24.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:24.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:24.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:24.854][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:24.855][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:24.856][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:24.857][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:24.858][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:24.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:24.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:24.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:24.862][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:24.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:24.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:24.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:24.866][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:24.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:24.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:24.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:24.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:24.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:24.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:24.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:24.911][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:24.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:24.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:24.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:24.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:24.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:24.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:24.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:24.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:24.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:24.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:24.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:24.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:24.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:24.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:24.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:24.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:24.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:24.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:24.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:24.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:24.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:24.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:24.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:24.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:24.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:24.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:24.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:24.938][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-06-26 21:02:24.939][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:24.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:24.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:24.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:24.943][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:24.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:24.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:24.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:24.947][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:24.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:24.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:24.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:24.950][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:24.951][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:24.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:24.956][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:24.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:24.958][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:24.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:24.960][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-06-26 21:02:24.961][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-26 21:02:24.963][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.INFO [2024-06-26 21:02:24.964][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-06-26 21:02:24.965][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-26 21:02:24.966][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-26 21:02:24.967][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 21:02:24.968][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-26 21:02:24.969][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-26 21:02:24.970][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-26 21:02:24.972][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:24.973][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:24.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:24.979][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:24.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:24.980][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:24.981][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[2024-06-26 21:02:24.982][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-06-26 21:02:24.985][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:24.986][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:24.987][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-06-26 21:02:25.375][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-06-26 21:02:25.785][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:25.790][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-06-26 21:02:25.797][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-06-26 21:02:25.803][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-06-26 21:02:25.806][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-26 21:02:25.809][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-26 21:02:25.812][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-26 21:02:25.815][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:25.817][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:25.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:25.829][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:25.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:25.832][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:25.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:25.838][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:25.840][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:25.842][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:25.843][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:25.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:25.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:25.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:25.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:25.851][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:25.853][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:25.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:25.855][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:25.857][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:25.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:25.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:25.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:25.862][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:25.863][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:25.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:25.865][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:25.867][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:25.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:25.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:25.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:25.871][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:25.872][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:25.874][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:25.874][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:25.876][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:25.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:25.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:25.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:25.880][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:25.881][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:25.882][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:25.883][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:25.884][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:25.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:25.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:25.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:25.888][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:25.889][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:25.890][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:25.891][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:25.892][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:25.893][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:25.894][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:25.895][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:25.896][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:25.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:25.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:25.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:25.900][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:25.901][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:25.901][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:25.902][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:25.904][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:25.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:25.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:25.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:25.917][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:25.918][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:25.919][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:25.920][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:25.921][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:25.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:25.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:25.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:25.925][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:25.926][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:25.927][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:25.928][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:25.929][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:25.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:25.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:25.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:25.933][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:25.934][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:25.935][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:25.936][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:25.938][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:25.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:25.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:25.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:25.942][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:25.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:25.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:25.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:25.945][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:25.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:25.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:25.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:25.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:25.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:25.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:25.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:25.953][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:25.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:25.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:25.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:25.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:25.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:25.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:25.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:25.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:25.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:25.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:25.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:25.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:25.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:25.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:25.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:25.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:25.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:25.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:25.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:25.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:25.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:25.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:25.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:25.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:25.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:25.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:25.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:25.980][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-06-26 21:02:25.981][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:25.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:25.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:25.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:25.984][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:25.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:25.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:25.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:25.988][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:25.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:25.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:25.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:25.992][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:25.993][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:25.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:25.998][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:25.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:25.999][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:26.000][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[2024-06-26 21:02:26.001][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-06-26 21:02:26.002][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-26 21:02:26.004][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-06-26 21:02:26.005][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-26 21:02:26.006][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-26 21:02:26.007][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 21:02:26.008][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-26 21:02:26.009][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-26 21:02:26.010][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-26 21:02:26.013][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:26.013][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:26.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:26.019][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:26.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:26.020][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:26.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:26.022][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-06-26 21:02:26.025][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:26.026][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:26.027][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-06-26 21:02:26.417][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-06-26 21:02:26.810][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:26.812][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-06-26 21:02:26.816][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-06-26 21:02:26.818][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-06-26 21:02:26.819][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-26 21:02:26.821][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-26 21:02:26.822][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-26 21:02:26.824][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:26.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:26.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:26.830][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:26.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:26.832][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:26.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:26.835][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:26.836][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:26.837][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:26.838][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:26.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:26.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:26.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:26.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:26.843][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:26.844][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:26.844][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:26.845][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:26.847][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:26.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:26.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:26.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:26.850][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:26.851][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:26.852][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:26.853][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:26.854][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:26.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:26.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:26.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:26.858][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:26.859][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:26.860][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:26.861][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:26.862][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:26.863][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:26.869][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:26.874][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:26.875][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:26.876][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:26.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:26.878][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:26.879][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:26.880][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:26.881][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:26.882][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:26.883][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:26.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:26.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:26.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:26.887][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:26.888][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:26.889][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:26.890][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:26.891][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:26.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:26.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:26.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:26.895][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:26.896][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:26.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:26.897][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:26.899][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:26.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:26.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:26.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:26.903][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:26.904][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:26.905][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:26.905][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:26.907][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:26.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:26.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:26.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:26.911][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:26.912][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:26.912][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:26.913][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:26.915][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:26.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:26.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:26.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:26.918][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:26.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:26.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:26.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:26.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:26.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:26.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:26.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:26.926][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:26.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:26.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:26.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:26.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:26.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:26.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:26.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:26.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:26.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:26.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:26.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:26.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:26.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:26.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:26.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:26.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:26.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:26.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:26.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:26.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:26.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:26.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:26.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:26.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:26.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:26.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:26.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:26.952][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-06-26 21:02:26.953][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:26.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:26.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:26.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:26.957][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:26.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:26.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:26.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:26.961][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:26.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:26.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:26.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:26.965][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:26.965][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:26.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:26.971][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:26.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:26.972][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:26.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:26.974][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-06-26 21:02:26.975][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-26 21:02:26.977][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-06-26 21:02:26.978][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-26 21:02:26.979][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-26 21:02:26.980][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 21:02:26.981][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-26 21:02:26.982][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-26 21:02:26.983][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-26 21:02:26.985][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:26.986][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:26.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:26.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:26.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:26.993][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:26.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:26.995][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-06-26 21:02:26.998][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:26.999][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:27.001][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-06-26 21:02:27.386][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2024-06-26 21:02:27.775][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2024-06-26 21:02:27.779][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-06-26 21:02:27.782][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-06-26 21:02:27.789][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-06-26 21:02:27.795][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-06-26 21:02:27.798][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-26 21:02:27.801][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-26 21:02:27.803][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-26 21:02:27.807][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:27.808][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:27.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:27.819][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:27.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:27.823][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:27.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:27.828][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:27.829][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:27.831][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:27.832][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:27.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:27.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:27.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:27.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:27.840][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:27.841][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:27.843][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:27.844][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:27.854][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:27.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:27.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:27.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:27.859][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:27.860][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:27.862][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:27.863][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:27.864][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:27.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:27.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:27.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:27.868][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:27.869][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:27.870][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:27.871][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:27.872][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:27.873][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:27.874][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:27.875][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:27.876][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:27.877][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:27.878][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:27.879][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:27.880][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:27.881][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:27.882][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:27.883][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:27.884][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:27.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:27.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:27.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:27.888][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:27.889][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:27.890][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:27.891][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:27.892][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:27.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:27.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:27.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:27.896][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:27.897][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:27.898][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:27.898][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:27.900][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:27.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:27.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:27.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:27.904][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:27.905][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:27.905][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:27.906][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:27.908][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:27.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:27.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:27.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:27.911][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:27.913][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:27.913][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:27.914][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:27.916][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:27.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:27.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:27.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:27.919][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:27.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:27.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:27.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:27.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:27.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:27.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:27.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:27.927][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:27.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:27.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:27.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:27.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:27.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:27.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:27.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:27.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:27.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:27.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:27.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:27.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:27.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:27.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:27.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:27.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:27.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:27.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:27.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:27.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:27.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:27.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:27.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:27.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:27.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:27.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:27.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:27.953][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-06-26 21:02:27.954][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:27.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:27.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:27.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:27.958][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:27.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:27.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:27.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:27.962][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:27.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:27.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:27.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:27.965][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:27.966][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:27.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:27.971][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:27.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:27.973][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:27.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:27.975][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-06-26 21:02:27.976][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-26 21:02:27.977][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-06-26 21:02:27.979][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-26 21:02:27.980][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-26 21:02:27.981][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 21:02:27.982][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-26 21:02:27.983][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-26 21:02:27.983][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-26 21:02:27.986][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:27.987][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:27.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:27.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:27.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:27.994][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:27.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:27.996][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-06-26 21:02:27.998][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:27.999][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:28.001][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-06-26 21:02:28.400][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2024-06-26 21:02:28.790][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:28.792][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-06-26 21:02:28.796][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-06-26 21:02:28.798][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-06-26 21:02:28.800][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-26 21:02:28.801][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-26 21:02:28.802][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-26 21:02:28.804][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:28.805][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:28.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:28.819][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:28.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:28.821][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:28.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:28.825][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:28.826][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:28.827][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:28.828][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:28.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:28.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:28.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:28.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:28.833][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:28.834][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:28.835][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:28.836][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:28.838][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:28.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:28.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:28.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:28.842][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:28.843][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:28.844][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:28.845][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:28.846][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:28.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:28.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:28.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:28.850][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:28.851][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:28.852][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:28.853][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:28.854][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:28.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:28.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:28.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:28.858][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:28.859][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:28.860][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:28.861][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:28.862][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:28.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:28.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:28.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:28.866][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:28.867][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:28.868][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:28.869][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:28.870][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:28.871][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:28.872][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:28.873][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:28.874][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:28.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:28.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:28.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:28.878][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:28.879][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:28.880][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:28.881][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:28.882][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:28.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:28.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:28.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:28.886][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:28.887][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:28.888][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:28.889][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:28.890][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:28.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:28.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:28.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:28.894][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:28.895][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:28.896][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:28.897][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:28.898][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:28.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:28.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:28.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:28.902][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:28.903][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:28.904][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:28.905][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:28.906][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:28.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:28.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:28.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:28.910][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:28.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:28.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:28.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:28.914][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:28.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:28.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:28.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:28.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:28.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:28.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:28.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:28.921][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:28.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:28.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:28.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:28.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:28.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:28.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:28.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:28.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:28.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:28.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:28.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:28.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:28.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:28.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:28.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:28.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:28.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:28.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:28.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:28.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:28.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:28.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:28.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:28.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:28.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:28.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:28.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:28.948][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-06-26 21:02:28.950][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:28.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:28.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:28.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:28.953][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:28.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:28.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:28.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:28.957][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:28.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:28.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:28.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:28.962][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:28.962][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:28.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:28.969][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:28.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:28.971][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:28.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:28.973][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-06-26 21:02:28.974][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-26 21:02:28.976][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-06-26 21:02:28.977][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-26 21:02:28.978][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-26 21:02:28.979][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 21:02:28.980][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-26 21:02:28.981][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-26 21:02:28.982][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-26 21:02:28.985][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:28.986][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:28.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:28.999][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:29.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:29.001][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:29.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:29.003][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-06-26 21:02:29.006][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:29.007][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:29.009][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-06-26 21:02:29.404][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-06-26 21:02:29.807][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:29.810][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-06-26 21:02:29.813][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-06-26 21:02:29.816][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-06-26 21:02:29.817][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-26 21:02:29.818][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-26 21:02:29.819][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-26 21:02:29.821][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:29.822][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:29.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:29.827][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:29.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:29.829][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:29.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:29.837][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:29.839][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:29.840][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:29.841][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:29.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:29.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:29.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:29.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:29.847][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:29.848][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:29.849][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:29.850][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:29.852][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:29.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:29.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:29.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:29.857][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:29.858][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:29.859][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:29.860][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:29.861][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:29.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:29.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:29.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:29.865][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:29.866][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:29.867][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:29.868][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:29.870][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:29.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:29.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:29.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:29.874][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:29.875][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:29.876][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:29.877][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:29.878][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:29.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:29.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:29.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:29.883][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:29.884][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:29.885][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:29.886][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:29.887][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:29.888][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:29.889][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:29.890][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:29.892][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:29.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:29.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:29.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:29.896][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:29.897][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:29.898][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:29.899][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:29.900][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:29.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:29.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:29.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:29.904][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:29.906][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:29.907][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:29.908][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:29.909][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:29.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:29.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:29.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:29.913][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:29.914][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:29.915][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:29.916][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:29.918][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:29.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:29.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:29.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:29.922][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:29.923][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:29.924][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:29.925][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:29.926][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:29.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:29.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:29.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:29.931][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:29.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:29.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:29.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:29.935][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:29.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:29.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:29.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:29.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:29.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:29.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:29.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:29.943][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:29.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:29.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:29.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:29.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:29.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:29.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:29.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:29.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:29.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:29.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:29.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:29.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:29.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:29.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:29.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:29.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:29.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:29.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:29.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:29.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:29.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:29.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:29.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:29.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:29.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:29.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:29.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:29.972][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-06-26 21:02:29.973][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:29.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:29.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:29.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:29.977][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:29.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:29.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:29.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:29.999][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:30.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:30.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:30.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:30.004][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:30.005][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:30.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:30.010][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:30.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:30.012][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:30.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:30.014][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-06-26 21:02:30.015][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-26 21:02:30.017][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-06-26 21:02:30.018][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-26 21:02:30.019][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-26 21:02:30.021][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 21:02:30.022][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-26 21:02:30.023][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-26 21:02:30.024][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-26 21:02:30.026][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:30.027][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:30.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:30.033][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:30.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:30.034][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:30.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:30.037][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-06-26 21:02:30.039][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:30.040][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:30.042][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-06-26 21:02:30.444][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-06-26 21:02:30.871][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:30.873][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-06-26 21:02:30.877][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-06-26 21:02:30.879][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-06-26 21:02:30.880][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-26 21:02:30.882][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-26 21:02:30.883][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-26 21:02:30.884][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:30.885][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:30.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:30.890][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:30.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:30.892][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:30.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:30.896][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:30.897][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:30.898][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:30.899][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:30.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:30.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:30.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:30.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:30.904][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:30.905][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:30.906][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:30.907][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:30.908][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:30.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:30.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:30.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:30.912][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:30.913][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:30.914][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:30.915][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:30.916][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:30.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:30.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:30.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:30.920][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:30.921][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:30.922][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:30.923][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:30.924][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:30.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:30.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:30.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:30.928][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:30.929][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:30.930][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:30.931][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:30.932][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:30.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:30.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:30.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:30.936][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:30.937][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:30.938][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:30.938][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:30.940][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:30.941][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:30.942][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:30.942][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:30.944][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:30.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:30.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:30.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:30.947][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:30.948][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:30.949][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:30.950][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:30.951][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:30.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:30.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:30.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:30.955][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:30.956][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:30.957][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:30.958][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:30.959][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:30.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:30.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:30.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:30.963][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:30.964][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:30.965][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:30.966][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:30.967][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:30.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:30.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:30.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:30.971][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:30.972][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:30.973][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:30.974][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:30.975][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:30.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:30.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:30.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:30.979][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:30.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:30.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:30.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:30.982][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:30.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:30.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:30.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:30.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:30.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:30.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:30.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:30.990][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:30.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:30.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:30.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:30.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:30.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:31.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:31.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:31.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:31.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:31.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:31.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:31.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:31.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:31.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:31.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:31.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:31.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:31.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:31.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:31.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:31.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:31.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:31.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:31.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:31.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:31.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:31.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:31.024][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-06-26 21:02:31.025][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:31.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:31.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:31.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:31.029][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:31.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:31.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:31.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:31.033][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:31.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:31.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:31.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:31.036][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:31.037][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:31.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:31.042][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:31.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:31.044][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:31.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:31.046][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-06-26 21:02:31.047][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-26 21:02:31.049][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-06-26 21:02:31.050][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-26 21:02:31.051][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-26 21:02:31.052][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 21:02:31.053][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-26 21:02:31.054][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-26 21:02:31.055][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-26 21:02:31.057][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:31.058][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:31.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:31.063][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:31.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:31.065][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:31.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:31.067][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-06-26 21:02:31.069][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:31.070][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:31.071][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-06-26 21:02:31.488][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-06-26 21:02:31.956][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:31.958][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-06-26 21:02:31.962][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-06-26 21:02:31.964][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-06-26 21:02:31.965][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-26 21:02:31.966][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-26 21:02:31.967][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-26 21:02:31.969][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:31.970][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:31.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:31.975][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:31.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:31.976][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:31.977][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.TRACE[2024-06-26 21:02:31.979][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:31.980][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:31.981][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:31.982][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:31.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:31.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:31.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:31.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:31.987][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:31.988][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:31.989][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:31.990][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:31.991][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:31.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:31.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:31.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:31.995][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:31.996][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:31.997][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:31.998][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:31.999][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:32.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:32.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.003][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:32.004][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:32.005][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.005][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.007][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:32.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:32.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.010][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:32.011][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:32.012][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.013][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.014][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:32.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:32.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.018][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:32.019][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:32.020][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.021][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.022][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:32.023][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:32.024][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.025][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.026][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:32.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:32.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.030][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:32.031][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:32.032][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.033][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.034][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:32.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:32.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.038][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:32.039][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:32.040][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.041][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.042][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:32.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:32.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.046][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:32.047][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:32.048][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.053][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.059][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:32.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:32.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.062][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:32.063][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:32.064][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.065][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.066][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:32.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:32.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.070][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:32.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:32.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.074][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:32.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:32.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:32.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:32.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.081][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:32.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:32.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:32.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:32.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:32.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:32.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:32.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:32.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:32.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:32.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:32.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:32.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:32.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:32.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:32.107][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-06-26 21:02:32.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:32.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:32.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.112][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:32.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:32.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.116][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:32.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:32.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:32.119][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:32.120][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:32.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:32.125][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:32.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:32.127][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:32.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:32.129][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-06-26 21:02:32.130][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-26 21:02:32.131][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-06-26 21:02:32.132][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-26 21:02:32.133][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-26 21:02:32.134][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 21:02:32.135][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-26 21:02:32.136][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-26 21:02:32.137][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-26 21:02:32.140][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:32.141][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:32.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:32.146][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:32.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:32.147][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:32.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:32.149][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-06-26 21:02:32.152][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:32.153][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:32.154][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-06-26 21:02:32.539][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-06-26 21:02:32.924][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:32.926][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-06-26 21:02:32.929][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-06-26 21:02:32.931][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-06-26 21:02:32.933][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-26 21:02:32.934][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-26 21:02:32.935][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-26 21:02:32.936][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:32.937][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:32.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:32.942][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:32.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:32.944][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:32.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:32.947][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:32.948][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:32.949][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.950][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:32.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:32.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.955][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:32.956][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:32.957][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.958][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.959][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:32.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:32.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.963][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:32.964][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:32.965][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.965][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.967][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:32.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:32.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.970][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:32.971][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:32.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.973][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.974][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:32.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:32.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.978][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:32.979][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:32.980][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.981][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.982][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:32.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:32.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.986][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:32.994][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:32.995][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:32.996][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:32.997][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:32.998][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:32.999][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.000][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.001][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:33.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:33.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.005][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:33.006][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:33.007][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.009][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.010][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:33.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:33.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.015][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:33.016][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:33.017][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.018][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.019][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:33.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:33.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.023][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:33.024][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:33.025][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.026][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.027][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:33.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:33.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.031][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:33.032][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:33.033][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.034][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.035][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:33.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:33.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.039][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:33.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:33.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.043][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:33.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:33.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.046][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:33.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:33.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.050][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:33.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:33.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:33.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:33.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.057][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:33.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:33.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:33.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:33.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:33.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:33.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:33.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:33.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:33.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:33.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:33.076][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-06-26 21:02:33.077][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:33.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:33.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.081][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:33.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:33.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.084][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:33.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:33.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:33.088][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:33.089][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:33.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:33.094][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:33.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:33.096][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:33.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:33.098][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-06-26 21:02:33.099][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-26 21:02:33.100][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-06-26 21:02:33.101][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-26 21:02:33.102][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-26 21:02:33.103][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 21:02:33.104][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-26 21:02:33.105][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-26 21:02:33.106][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-26 21:02:33.108][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:33.109][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:33.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:33.114][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:33.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:33.116][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:33.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:33.118][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-06-26 21:02:33.121][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:33.122][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:33.123][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-06-26 21:02:33.510][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-06-26 21:02:33.897][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:33.900][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-06-26 21:02:33.903][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-06-26 21:02:33.906][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-06-26 21:02:33.907][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-26 21:02:33.909][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-26 21:02:33.910][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-26 21:02:33.912][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:33.912][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:33.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:33.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:33.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:33.919][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:33.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:33.922][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:33.923][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:33.924][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.925][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:33.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:33.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.930][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:33.931][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:33.941][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.942][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.943][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:33.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:33.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.947][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:33.948][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:33.949][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.950][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.952][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:33.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:33.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.955][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:33.957][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:33.957][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.958][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.960][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:33.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:33.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.964][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:33.965][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:33.965][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.966][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.968][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:33.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:33.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.971][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:33.972][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:33.973][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.974][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.975][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:33.976][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:33.977][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.978][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.980][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:33.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:33.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.983][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:33.984][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:33.985][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.986][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.987][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:33.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:33.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.991][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:33.992][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:33.993][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.994][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.996][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:33.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:33.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:33.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:33.999][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:34.000][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:34.001][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:34.002][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:34.003][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:34.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:34.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:34.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:34.007][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:34.008][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:34.009][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:34.010][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:34.011][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:34.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:34.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:34.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:34.015][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:34.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:34.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:34.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:34.019][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:34.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:34.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:34.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:34.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:34.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:34.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:34.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:34.027][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:34.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:34.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:34.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:34.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:34.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:34.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:34.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:34.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:34.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:34.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:34.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:34.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:34.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:34.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:34.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:34.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:34.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:34.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:34.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:34.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:34.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:34.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:34.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:34.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:34.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:34.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:34.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:34.054][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-06-26 21:02:34.056][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:34.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:34.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:34.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:34.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:34.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:34.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:34.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:34.063][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:34.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:34.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:34.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:34.067][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:34.068][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:34.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:34.073][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:34.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:34.075][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:34.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:34.077][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-06-26 21:02:34.078][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-26 21:02:34.080][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-06-26 21:02:34.081][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-26 21:02:34.082][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-26 21:02:34.083][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 21:02:34.084][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-26 21:02:34.085][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-26 21:02:34.086][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-26 21:02:34.089][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:34.089][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:34.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:34.095][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:34.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:34.096][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:34.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:34.098][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2024-06-26 21:02:34.101][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:34.102][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:34.103][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-06-26 21:02:34.487][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-06-26 21:02:34.913][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:34.931][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-06-26 21:02:34.938][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-06-26 21:02:34.943][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-06-26 21:02:34.947][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-26 21:02:34.949][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-26 21:02:34.952][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-26 21:02:34.955][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:34.957][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:34.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:34.967][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:34.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:34.970][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:34.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:34.975][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:34.976][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:34.977][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:34.979][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:34.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:34.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:34.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:34.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:34.986][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:34.987][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:34.988][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:34.989][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:34.991][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:34.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:34.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:34.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:34.995][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:34.996][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:34.997][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:34.998][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:35.000][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:35.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:35.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:35.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:35.004][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:35.005][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:35.006][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:35.007][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:35.008][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:35.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:35.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:35.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:35.012][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:35.013][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:35.014][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:35.015][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:35.016][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:35.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:35.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:35.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:35.020][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:35.021][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:35.021][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:35.022][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:35.024][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:35.025][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:35.025][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:35.026][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:35.027][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:35.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:35.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:35.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:35.031][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:35.032][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:35.033][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:35.034][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:35.035][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:35.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:35.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:35.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:35.039][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:35.040][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:35.041][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:35.042][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:35.043][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:35.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:35.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:35.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:35.047][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:35.048][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:35.049][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:35.050][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:35.051][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:35.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:35.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:35.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:35.054][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:35.055][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:35.056][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:35.057][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:35.058][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:35.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:35.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:35.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:35.062][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:35.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:35.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:35.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:35.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:35.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:35.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:35.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:35.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:35.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:35.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:35.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:35.073][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:35.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:35.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:35.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:35.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:35.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:35.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:35.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:35.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:35.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:35.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:35.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:35.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:35.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:35.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:35.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:35.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:35.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:35.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:35.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:35.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:35.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:35.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:35.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:35.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:35.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:35.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:35.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:35.099][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-06-26 21:02:35.100][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:35.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:35.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:35.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:35.104][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:35.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:35.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:35.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:35.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:35.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:35.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:35.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:35.132][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-26 21:02:35.135][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:35.136][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:35.138][private$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[2024-06-26 21:02:35.676][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[2024-06-26 21:02:36.253][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:36.257][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-06-26 21:02:36.265][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-06-26 21:02:36.273][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:36.275][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:36.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:36.286][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:36.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:36.290][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:36.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:36.295][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.302][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.309][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:36.315][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:36.317][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:36.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:36.324][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:36.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:36.326][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:36.327][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[2024-06-26 21:02:36.329][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.333][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.338][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.342][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.346][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:36.350][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:36.351][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:36.352][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:36.356][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:36.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:36.357][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:36.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:36.359][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.363][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.367][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.371][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.374][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:36.378][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:36.379][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:36.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:36.384][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:36.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:36.386][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:36.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:36.388][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.391][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.395][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.399][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.403][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:36.407][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:36.407][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:36.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:36.412][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:36.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:36.414][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:36.415][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.TRACE[2024-06-26 21:02:36.416][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.420][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.423][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:36.427][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:36.428][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:36.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:36.433][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:36.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:36.435][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:36.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:36.441][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.449][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.452][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:36.456][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:36.457][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:36.458][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:36.462][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:36.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:36.464][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:36.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:36.466][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.470][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.474][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:36.477][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:36.478][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:36.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:36.484][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:36.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:36.485][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:36.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:36.487][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.491][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.495][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:36.498][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:36.499][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:36.500][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:36.504][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:36.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:36.506][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:36.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:36.508][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.512][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.516][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:36.519][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:36.520][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:36.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:36.525][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:36.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:36.527][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:36.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:36.529][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.533][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.536][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:36.540][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:36.541][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:36.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:36.546][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:36.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:36.547][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:36.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:36.549][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.553][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.557][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:36.561][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:36.561][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:36.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:36.566][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:36.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:36.568][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:36.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:36.570][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.574][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.577][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:36.581][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:36.582][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:36.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:36.587][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:36.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:36.589][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:36.589][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.TRACE[2024-06-26 21:02:36.590][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.594][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.598][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:36.602][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:36.602][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:36.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:36.612][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:36.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:36.614][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:36.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:36.616][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.620][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.623][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:36.627][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:36.628][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:36.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:36.633][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:36.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:36.635][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:36.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:36.637][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.640][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.644][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:36.648][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:36.649][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:36.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:36.654][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:36.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:36.655][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:36.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:36.657][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.661][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.665][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:36.668][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:36.669][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:36.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:36.674][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:36.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:36.676][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:36.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:36.678][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.682][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.685][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:36.689][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:36.690][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:36.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:36.695][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:36.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:36.697][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:36.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:36.698][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.702][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.706][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:36.710][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:36.710][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:36.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:36.715][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:36.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:36.717][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:36.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:36.719][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.723][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.726][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:36.730][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:36.731][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:36.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:36.736][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:36.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:36.738][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:36.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:36.740][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.743][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.747][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:36.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:36.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:36.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:36.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:36.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.775][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:36.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:36.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.779][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:36.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:36.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:36.783][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:36.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:36.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:36.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:36.810][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[2024-06-26 21:02:36.814][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:36.815][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:36.816][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-26 21:02:37.203][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-26 21:02:37.632][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:37.640][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2024-06-26 21:02:37.650][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2024-06-26 21:02:37.660][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-26 21:02:37.668][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:37.670][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:37.674][private$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[2024-06-26 21:02:38.112][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[2024-06-26 21:02:38.599][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:38.604][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2024-06-26 21:02:38.612][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2024-06-26 21:02:38.619][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:38.621][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:38.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:38.636][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:38.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:38.641][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:38.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:38.645][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-06-26 21:02:38.647][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-26 21:02:38.650][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-06-26 21:02:38.652][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-26 21:02:38.654][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-26 21:02:38.656][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 21:02:38.658][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-26 21:02:38.660][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-26 21:02:38.661][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-26 21:02:38.665][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:38.667][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:38.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:38.674][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:38.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:38.676][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:38.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:38.679][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2024-06-26 21:02:38.682][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:38.683][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:38.685][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2024-06-26 21:02:39.125][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2024-06-26 21:02:39.562][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:39.567][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2024-06-26 21:02:39.574][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2024-06-26 21:02:39.581][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2024-06-26 21:02:39.584][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-26 21:02:39.587][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-26 21:02:39.590][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-26 21:02:39.594][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:39.596][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:39.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:39.608][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:39.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:39.611][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:39.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:39.617][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:39.619][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:39.621][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.622][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:39.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:39.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.630][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:39.632][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:39.633][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.634][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.636][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:39.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:39.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.641][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:39.642][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:39.644][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.645][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.646][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:39.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:39.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.651][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:39.652][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:39.674][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.675][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.677][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:39.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:39.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.681][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:39.682][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:39.683][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.684][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.685][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:39.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:39.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.690][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:39.691][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:39.692][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.693][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.694][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:39.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:39.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.698][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:39.699][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:39.700][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.701][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.702][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:39.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:39.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.706][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:39.707][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:39.708][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.709][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.710][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:39.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:39.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.715][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:39.716][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:39.717][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.717][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.719][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:39.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:39.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.723][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:39.724][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:39.725][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.726][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.727][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:39.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:39.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.731][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:39.732][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:39.733][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.734][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.735][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:39.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:39.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.739][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:39.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:39.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.743][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:39.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:39.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:39.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:39.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.750][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:39.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:39.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:39.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:39.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:39.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:39.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:39.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:39.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:39.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:39.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:39.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:39.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:39.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:39.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:39.776][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-06-26 21:02:39.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:39.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:39.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.781][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:39.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:39.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.785][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:39.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:39.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:39.789][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:39.789][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:39.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:39.794][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:39.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:39.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:39.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:39.798][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:39.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:39.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.802][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:39.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:39.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:39.806][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:39.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:39.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:39.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:39.809][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:39.810][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:39.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:39.815][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:39.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:39.817][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:39.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:39.819][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-06-26 21:02:39.820][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-26 21:02:39.822][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-06-26 21:02:39.823][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-26 21:02:39.824][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-26 21:02:39.825][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 21:02:39.826][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-26 21:02:39.827][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-26 21:02:39.828][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-26 21:02:39.830][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:39.831][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:39.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:39.836][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:39.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:39.842][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:39.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:39.845][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2024-06-26 21:02:39.848][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:39.848][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:39.850][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2024-06-26 21:02:40.237][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2024-06-26 21:02:40.622][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:40.625][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2024-06-26 21:02:40.628][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2024-06-26 21:02:40.631][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2024-06-26 21:02:40.632][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-26 21:02:40.634][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-26 21:02:40.635][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-26 21:02:40.636][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:40.637][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:40.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:40.643][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:40.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:40.644][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:40.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:40.647][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:40.648][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:40.649][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.650][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:40.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:40.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.655][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:40.656][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:40.657][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.658][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.660][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:40.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:40.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.663][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:40.664][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:40.665][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.666][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.667][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:40.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:40.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.671][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:40.672][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:40.673][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.674][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.675][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:40.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:40.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.679][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:40.680][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:40.681][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.682][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.683][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:40.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:40.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.687][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:40.688][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:40.689][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.689][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.691][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:40.692][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:40.692][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.693][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.695][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:40.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:40.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.698][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.699][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.700][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.701][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.702][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.706][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:40.707][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:40.708][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.709][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.710][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:40.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:40.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.714][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:40.715][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:40.716][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.717][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.718][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:40.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:40.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.722][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:40.723][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:40.724][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.724][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.726][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:40.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:40.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.729][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:40.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:40.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.733][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:40.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:40.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:40.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:40.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.741][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:40.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:40.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:40.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:40.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:40.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:40.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:40.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:40.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:40.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:40.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:40.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:40.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:40.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:40.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:40.767][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-06-26 21:02:40.768][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.772][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.780][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:40.804][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[2024-06-26 21:02:40.808][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-26 21:02:40.809][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-26 21:02:40.810][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 21:02:40.812][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-26 21:02:40.815][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:40.815][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:40.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:40.821][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:40.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:40.822][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:40.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:40.824][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.828][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.832][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:40.836][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:40.837][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:40.837][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:40.842][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:40.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:40.843][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:40.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:40.845][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.849][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.853][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.857][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.861][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:40.864][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:40.865][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:40.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:40.870][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:40.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:40.872][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:40.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:40.874][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.878][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.882][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.886][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.889][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:40.893][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:40.894][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:40.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:40.899][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:40.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:40.901][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:40.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:40.903][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.907][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.911][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.915][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.918][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:40.922][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:40.923][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:40.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:40.928][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:40.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:40.930][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:40.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:40.932][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.936][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.940][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:40.943][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:40.944][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:40.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:40.955][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:40.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:40.957][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:40.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:40.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.962][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.966][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:40.970][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:40.971][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:40.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:40.976][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:40.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:40.978][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:40.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:40.980][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.984][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:40.988][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:40.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:40.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:40.992][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:40.992][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:40.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:40.998][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:40.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:40.999][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:41.000][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.TRACE[2024-06-26 21:02:41.001][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.005][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.009][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:41.012][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:41.013][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:41.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:41.018][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:41.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:41.020][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:41.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:41.022][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.026][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.029][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:41.033][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:41.034][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:41.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:41.039][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:41.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:41.041][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:41.042][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[2024-06-26 21:02:41.043][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.046][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.050][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:41.054][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:41.055][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:41.056][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:41.060][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:41.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:41.061][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:41.062][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.TRACE[2024-06-26 21:02:41.063][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.067][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.071][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:41.075][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:41.075][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:41.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:41.081][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:41.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:41.082][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:41.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:41.084][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.088][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.092][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:41.095][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:41.096][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:41.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:41.101][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:41.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:41.103][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:41.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:41.105][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.108][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:41.122][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:41.123][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:41.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:41.128][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:41.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:41.130][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:41.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:41.132][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.136][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.140][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:41.143][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:41.144][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:41.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:41.149][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:41.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:41.151][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:41.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:41.153][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.157][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.161][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:41.165][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:41.165][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:41.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:41.171][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:41.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:41.172][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:41.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:41.174][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.178][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.182][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:41.185][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:41.186][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:41.187][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:41.191][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:41.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:41.193][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:41.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:41.195][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.198][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.202][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:41.206][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:41.207][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:41.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:41.211][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:41.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:41.213][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:41.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:41.215][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.219][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.222][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:41.226][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:41.227][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:41.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:41.232][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:41.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:41.233][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:41.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:41.235][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.239][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.243][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:41.247][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:41.247][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:41.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:41.253][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:41.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:41.254][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:41.255][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.TRACE[2024-06-26 21:02:41.256][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.260][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.264][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:41.290][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[2024-06-26 21:02:41.293][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-26 21:02:41.295][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-26 21:02:41.296][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 21:02:41.297][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-26 21:02:41.300][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:41.301][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:41.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:41.306][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:41.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:41.307][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:41.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:41.309][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.313][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.317][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:41.321][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:41.321][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:41.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:41.327][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:41.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:41.328][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:41.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:41.330][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.334][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.338][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.341][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.345][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:41.349][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:41.350][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:41.351][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:41.355][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:41.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:41.356][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:41.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:41.358][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.362][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.366][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.370][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.373][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:41.377][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:41.378][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:41.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:41.383][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:41.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:41.384][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:41.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:41.386][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.390][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.394][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.398][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.401][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:41.405][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:41.406][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:41.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:41.411][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:41.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:41.413][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:41.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:41.415][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.418][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.422][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:41.426][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:41.427][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:41.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:41.432][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:41.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:41.434][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:41.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:41.435][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.439][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.443][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:41.447][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:41.448][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:41.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:41.459][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:41.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:41.461][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:41.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:41.463][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.466][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.470][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:41.474][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:41.475][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:41.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:41.480][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:41.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:41.482][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:41.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:41.484][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.487][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.491][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:41.495][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:41.496][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:41.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:41.501][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:41.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:41.503][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:41.504][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.TRACE[2024-06-26 21:02:41.505][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.509][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.512][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:41.516][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:41.517][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:41.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:41.522][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:41.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:41.524][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:41.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:41.526][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.530][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:41.537][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:41.538][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:41.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:41.543][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:41.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:41.545][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:41.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:41.547][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.551][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.555][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:41.558][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:41.559][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:41.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:41.565][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:41.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:41.566][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:41.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:41.568][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.572][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.576][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:41.580][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:41.581][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:41.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:41.586][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:41.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:41.588][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:41.589][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.TRACE[2024-06-26 21:02:41.590][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.594][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.598][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:41.602][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:41.603][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:41.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:41.608][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:41.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:41.610][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:41.610][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.TRACE[2024-06-26 21:02:41.612][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.615][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.619][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:41.628][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:41.629][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:41.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:41.634][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:41.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:41.636][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:41.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:41.638][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.642][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.646][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:41.649][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:41.650][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:41.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:41.655][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:41.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:41.657][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:41.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:41.659][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.663][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:41.670][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:41.671][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:41.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:41.676][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:41.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:41.678][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:41.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:41.680][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.683][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.687][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:41.691][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:41.692][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:41.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:41.697][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:41.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:41.698][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:41.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:41.700][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.708][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:41.712][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:41.712][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:41.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:41.718][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:41.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:41.719][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:41.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:41.721][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.725][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.729][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:41.733][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:41.733][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:41.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:41.739][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:41.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:41.740][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:41.741][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.TRACE[2024-06-26 21:02:41.742][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.750][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:41.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.765][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-26 21:02:41.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-26 21:02:41.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-26 21:02:41.775][biodb::testThat]
biodb.INFO [2024-06-26 21:02:41.776][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-06-26 21:02:41.777][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:02:41.778][biodb::testThat]
biodb.TRACE[2024-06-26 21:02:41.781][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-26 21:02:41.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-26 21:02:41.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.784][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:41.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:41.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.793][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:41.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:41.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.797][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:41.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:41.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:41.801][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:41.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:41.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:41.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:41.808][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:41.809][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:41.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:41.814][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:41.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:41.816][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:41.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:41.819][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[2024-06-26 21:02:41.822][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:41.823][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:41.825][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-26 21:02:42.226][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-26 21:02:42.614][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:42.617][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-06-26 21:02:42.620][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-06-26 21:02:42.623][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:42.624][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:42.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:42.629][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:42.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:42.631][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:42.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:42.633][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:42.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:42.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:42.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:42.637][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:42.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:42.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:42.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:42.640][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:42.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:42.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:42.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:42.645][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-26 21:02:42.648][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:42.649][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:42.650][private$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[2024-06-26 21:02:43.050][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[2024-06-26 21:02:43.436][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:43.438][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-06-26 21:02:43.442][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-06-26 21:02:43.445][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:43.445][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:43.446][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:43.451][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:43.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:43.452][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:43.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:43.454][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:43.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:43.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:43.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:43.458][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:43.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:43.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:43.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:43.462][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:43.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:43.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:43.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:43.466][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:43.466][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:43.467][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:43.471][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:43.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:43.473][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:43.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:43.475][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:43.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:43.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:43.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:43.478][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:43.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:43.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:43.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:43.482][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:43.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:43.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:43.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:43.486][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-26 21:02:43.488][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:43.488][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:43.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:43.493][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:43.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:43.495][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:43.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:43.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:43.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:43.501][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:43.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:43.504][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:43.505][private$selectFields]
biodb.TRACE[2024-06-26 21:02:43.506][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 21:02:43.507][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 21:02:43.508][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:43.509][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.510][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.510][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:43.511][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:43.512][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.513][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.514][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:43.515][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:43.516][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:43.517][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:43.518][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.519][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.520][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:43.520][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:43.521][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-26 21:02:43.522][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:43.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:43.537][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:43.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:43.541][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:43.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:43.554][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-06-26 21:02:43.555][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:43.556][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:43.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:43.561][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:43.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:43.562][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:43.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:43.564][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:43.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:43.568][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:43.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:43.572][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:43.573][private$selectFields]
biodb.TRACE[2024-06-26 21:02:43.574][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 21:02:43.575][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 21:02:43.575][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:43.576][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.577][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.578][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:43.579][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:43.580][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.581][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.582][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:43.583][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:43.584][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:43.585][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:43.586][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.587][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.587][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:43.588][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:43.589][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-26 21:02:43.590][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:43.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:43.594][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:43.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:43.598][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:43.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:43.602][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-26 21:02:43.603][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:43.603][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:43.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:43.608][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:43.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:43.610][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:43.611][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[2024-06-26 21:02:43.612][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:43.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:43.616][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:43.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:43.619][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:43.620][private$selectFields]
biodb.TRACE[2024-06-26 21:02:43.621][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 21:02:43.622][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 21:02:43.623][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:43.624][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.625][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.626][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:43.627][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:43.628][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.628][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.629][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:43.630][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:43.631][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:43.632][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:43.633][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.634][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.635][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:43.636][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:43.637][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-26 21:02:43.638][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:43.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:43.641][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:43.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:43.645][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:43.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:43.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:43.649][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-06-26 21:02:43.650][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-26 21:02:43.651][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-26 21:02:43.660][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:43.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:43.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:43.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:43.663][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:43.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:43.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:43.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:43.667][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:43.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:43.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:43.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:43.671][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:43.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:43.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:43.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:43.732][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:43.733][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:43.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:43.738][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:43.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:43.740][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:43.740][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[2024-06-26 21:02:43.743][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[2024-06-26 21:02:43.746][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:43.747][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:43.749][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-26 21:02:44.170][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-26 21:02:44.562][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:44.564][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-06-26 21:02:44.568][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-06-26 21:02:44.571][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-26 21:02:44.574][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:44.575][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:44.577][private$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[2024-06-26 21:02:44.969][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[2024-06-26 21:02:45.360][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:45.362][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-06-26 21:02:45.365][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-06-26 21:02:45.368][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:45.369][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:45.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:45.375][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:45.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:45.376][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:45.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:45.378][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:45.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:45.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.382][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:45.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:45.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.386][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:45.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:45.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:45.390][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:45.391][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:45.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:45.396][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:45.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:45.398][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:45.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:45.400][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:45.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:45.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.404][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:45.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:45.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.408][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:45.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:45.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:45.412][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:45.413][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:45.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:45.418][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:45.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:45.419][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:45.420][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.TRACE[2024-06-26 21:02:45.421][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:45.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:45.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.425][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:45.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:45.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.429][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:45.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:45.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:45.465][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-26 21:02:45.488][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:45.489][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:45.490][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:45.494][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:45.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:45.496][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:45.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:45.498][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.502][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.505][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:45.506][private$selectFields]
biodb.TRACE[2024-06-26 21:02:45.507][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 21:02:45.508][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 21:02:45.509][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:45.510][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.511][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.512][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.513][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.514][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.515][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.516][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.516][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.517][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:45.518][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:45.519][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.520][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.521][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.522][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.523][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-26 21:02:45.524][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.528][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.531][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.535][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-06-26 21:02:45.536][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:45.537][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:45.538][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:45.542][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:45.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:45.544][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:45.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:45.557][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.561][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.608][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:45.610][private$selectFields]
biodb.TRACE[2024-06-26 21:02:45.612][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 21:02:45.614][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 21:02:45.615][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:45.617][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.618][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.619][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.620][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.621][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.622][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.623][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.624][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.625][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:45.637][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:45.638][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.639][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.640][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.641][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.642][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-26 21:02:45.643][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.647][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.651][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.656][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-26 21:02:45.657][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:45.658][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:45.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:45.663][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:45.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:45.665][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:45.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:45.667][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.671][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.675][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:45.676][private$selectFields]
biodb.TRACE[2024-06-26 21:02:45.677][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 21:02:45.678][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 21:02:45.679][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:45.680][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.681][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.682][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.683][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.684][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.685][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.686][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.687][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.688][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:45.689][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:45.690][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.691][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.692][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.693][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.694][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-26 21:02:45.695][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.699][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.703][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.707][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-06-26 21:02:45.708][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-26 21:02:45.709][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-26 21:02:45.717][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-26 21:02:45.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-26 21:02:45.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-26 21:02:45.725][biodb::testThat]
biodb.INFO [2024-06-26 21:02:45.726][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-06-26 21:02:45.727][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:02:45.728][biodb::testThat]
biodb.TRACE[2024-06-26 21:02:45.731][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-26 21:02:45.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-26 21:02:45.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.735][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:45.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:45.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.739][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:45.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:45.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.743][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:45.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:45.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.747][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:45.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:45.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:45.753][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:45.754][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:45.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:45.760][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:45.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:45.761][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:45.762][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[2024-06-26 21:02:45.765][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[2024-06-26 21:02:45.768][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-26 21:02:45.770][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-06-26 21:02:45.771][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 21:02:45.772][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-06-26 21:02:45.774][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:45.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:45.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:45.780][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:45.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:45.782][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:45.788][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[2024-06-26 21:02:45.790][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:45.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:45.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.794][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:45.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:45.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.797][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:45.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:45.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:45.802][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[2024-06-26 21:02:45.805][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-26 21:02:45.806][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-06-26 21:02:45.808][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 21:02:45.809][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-06-26 21:02:45.811][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:45.812][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:45.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:45.817][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:45.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:45.819][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:45.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:45.821][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:45.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:45.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.824][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:45.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:45.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.828][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:45.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:45.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:45.832][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:45.833][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:45.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:45.838][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:45.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:45.840][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:45.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:45.842][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:45.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:45.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.845][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:45.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:45.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.849][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:45.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:45.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:45.853][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-26 21:02:45.855][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:45.855][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:45.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:45.860][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:45.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:45.862][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:45.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:45.864][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.868][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.872][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:45.873][private$selectFields]
biodb.TRACE[2024-06-26 21:02:45.873][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 21:02:45.874][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 21:02:45.875][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:45.876][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.877][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.878][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.879][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.880][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.881][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.882][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.883][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.884][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:45.885][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:45.886][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.887][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.887][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.888][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.889][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-26 21:02:45.890][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.894][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.898][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.902][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-06-26 21:02:45.903][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:45.904][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:45.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:45.909][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:45.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:45.910][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:45.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:45.912][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.916][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.920][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:45.921][private$selectFields]
biodb.TRACE[2024-06-26 21:02:45.922][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 21:02:45.923][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 21:02:45.923][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:45.924][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.925][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.926][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.927][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.928][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.929][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.930][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.931][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.932][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:45.933][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:45.934][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.935][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.935][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.936][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.937][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-26 21:02:45.938][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.942][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.946][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.955][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-26 21:02:45.956][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:45.957][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:45.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:45.962][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:45.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:45.964][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:45.965][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[2024-06-26 21:02:45.966][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.970][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.974][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:45.975][private$selectFields]
biodb.TRACE[2024-06-26 21:02:45.975][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 21:02:45.976][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 21:02:45.977][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:45.978][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.979][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.980][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.981][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.982][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.983][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.984][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.985][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.986][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:45.987][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:45.988][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.989][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.989][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.990][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.991][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-26 21:02:45.992][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:45.996][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:45.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:45.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.000][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.004][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-06-26 21:02:46.005][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-26 21:02:46.006][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-26 21:02:46.013][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.017][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.021][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.025][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:46.030][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:46.031][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:46.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:46.036][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:46.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:46.038][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:46.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:46.041][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[2024-06-26 21:02:46.044][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-26 21:02:46.046][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-06-26 21:02:46.047][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 21:02:46.048][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-06-26 21:02:46.051][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[2024-06-26 21:02:46.054][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-26 21:02:46.055][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-06-26 21:02:46.056][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 21:02:46.058][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-06-26 21:02:46.060][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:46.061][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:46.062][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:46.066][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:46.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:46.067][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:46.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:46.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.073][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.077][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:46.081][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:46.082][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:46.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:46.087][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:46.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:46.089][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:46.090][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.TRACE[2024-06-26 21:02:46.091][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.095][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.099][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:46.102][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:46.103][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:46.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:46.108][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:46.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:46.110][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:46.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:46.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.121][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.126][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:46.129][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-26 21:02:46.131][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:46.132][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:46.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:46.137][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:46.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:46.138][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:46.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:46.140][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.144][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.148][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.149][private$selectFields]
biodb.TRACE[2024-06-26 21:02:46.150][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 21:02:46.151][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 21:02:46.151][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.152][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.153][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.154][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.155][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.156][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.157][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.158][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.159][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.160][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.161][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.162][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.163][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.163][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.164][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.165][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-26 21:02:46.166][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.170][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.174][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.178][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-06-26 21:02:46.179][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:46.179][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:46.180][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:46.184][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:46.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:46.186][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:46.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:46.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.192][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.195][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.196][private$selectFields]
biodb.TRACE[2024-06-26 21:02:46.197][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 21:02:46.198][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 21:02:46.199][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.200][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.201][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.202][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.203][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.203][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.204][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.205][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.206][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.207][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.208][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.209][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.210][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.211][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.212][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.213][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-26 21:02:46.214][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.217][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.221][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.225][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-26 21:02:46.226][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:46.227][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:46.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:46.232][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:46.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:46.234][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:46.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:46.236][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.239][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.243][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.244][private$selectFields]
biodb.TRACE[2024-06-26 21:02:46.245][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 21:02:46.246][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 21:02:46.247][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.248][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.249][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.250][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.250][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.251][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.252][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.254][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.255][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.256][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.257][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.258][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.259][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.260][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.260][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-26 21:02:46.261][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.265][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.269][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.273][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-06-26 21:02:46.274][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-26 21:02:46.275][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-26 21:02:46.287][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-26 21:02:46.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-26 21:02:46.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-26 21:02:46.294][biodb::testThat]
biodb.INFO [2024-06-26 21:02:46.295][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-06-26 21:02:46.296][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:02:46.297][biodb::testThat]
biodb.TRACE[2024-06-26 21:02:46.299][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-26 21:02:46.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-26 21:02:46.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.303][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:46.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:46.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.307][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:46.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:46.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.310][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:46.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:46.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.314][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:46.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:46.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:46.322][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:46.323][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:46.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:46.328][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:46.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:46.329][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:46.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:46.333][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[2024-06-26 21:02:46.336][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-26 21:02:46.337][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-06-26 21:02:46.338][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 21:02:46.339][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-06-26 21:02:46.342][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:46.343][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:46.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:46.347][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:46.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:46.349][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:46.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:46.351][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:46.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:46.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.355][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:46.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:46.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.359][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:46.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:46.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:46.363][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[2024-06-26 21:02:46.366][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-26 21:02:46.367][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-06-26 21:02:46.368][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 21:02:46.370][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-06-26 21:02:46.372][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:46.372][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:46.373][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:46.377][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:46.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:46.379][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:46.380][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.TRACE[2024-06-26 21:02:46.381][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:46.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:46.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.385][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:46.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:46.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.388][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:46.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:46.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:46.392][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:46.393][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:46.394][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:46.398][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:46.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:46.400][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:46.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:46.402][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:46.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:46.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.406][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:46.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:46.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.409][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:46.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:46.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:46.413][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-26 21:02:46.415][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:46.416][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:46.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:46.421][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:46.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:46.423][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:46.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:46.424][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.428][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.432][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.433][private$selectFields]
biodb.TRACE[2024-06-26 21:02:46.434][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 21:02:46.435][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 21:02:46.435][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.436][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.437][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.438][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.439][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.440][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.441][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.442][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.448][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.449][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.450][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.451][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.452][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.453][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.454][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.455][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-26 21:02:46.456][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.460][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.464][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.468][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-06-26 21:02:46.469][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:46.470][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:46.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:46.475][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:46.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:46.476][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:46.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:46.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.482][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.486][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.487][private$selectFields]
biodb.TRACE[2024-06-26 21:02:46.488][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 21:02:46.489][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 21:02:46.489][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.490][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.491][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.492][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.493][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.494][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.495][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.496][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.497][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.498][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.499][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.500][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.501][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.502][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.502][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.503][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-26 21:02:46.504][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.508][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.512][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.516][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-26 21:02:46.517][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:46.518][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:46.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:46.523][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:46.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:46.524][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:46.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:46.526][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.530][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.534][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.535][private$selectFields]
biodb.TRACE[2024-06-26 21:02:46.536][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 21:02:46.537][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 21:02:46.537][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.538][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.539][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.540][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.541][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.542][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.543][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.544][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.545][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.546][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.547][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.548][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.549][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.550][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.551][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.552][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-26 21:02:46.553][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.556][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.560][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.564][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-06-26 21:02:46.565][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-26 21:02:46.566][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-26 21:02:46.583][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.587][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.591][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.594][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:46.601][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:46.602][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:46.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:46.612][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:46.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:46.614][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:46.615][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[2024-06-26 21:02:46.617][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[2024-06-26 21:02:46.620][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-26 21:02:46.621][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-06-26 21:02:46.622][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 21:02:46.624][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-06-26 21:02:46.626][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[2024-06-26 21:02:46.629][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-26 21:02:46.631][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-06-26 21:02:46.632][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 21:02:46.633][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-06-26 21:02:46.635][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:46.636][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:46.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:46.641][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:46.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:46.643][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:46.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:46.644][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.648][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.652][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:46.656][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:46.657][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:46.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:46.662][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:46.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:46.663][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:46.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:46.665][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.669][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.673][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:46.677][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:46.677][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:46.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:46.682][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:46.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:46.684][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:46.685][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.TRACE[2024-06-26 21:02:46.686][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.690][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.693][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:46.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:46.697][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-26 21:02:46.699][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:46.700][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:46.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:46.705][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:46.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:46.706][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:46.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:46.708][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.712][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.716][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.716][private$selectFields]
biodb.TRACE[2024-06-26 21:02:46.717][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 21:02:46.718][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 21:02:46.719][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.720][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.721][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.722][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.723][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.724][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.725][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.726][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.727][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.727][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.728][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.729][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.730][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.731][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.732][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.733][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-26 21:02:46.734][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.738][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.741][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.746][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-06-26 21:02:46.747][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:46.747][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:46.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:46.752][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:46.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:46.754][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:46.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:46.756][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.760][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.763][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.764][private$selectFields]
biodb.TRACE[2024-06-26 21:02:46.765][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 21:02:46.766][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 21:02:46.767][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.773][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.775][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.776][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.777][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.778][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.779][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.780][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.781][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.781][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.782][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.783][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.784][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.785][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.786][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.787][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-26 21:02:46.788][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.792][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.796][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.800][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-26 21:02:46.801][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:46.802][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:46.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:46.807][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:46.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:46.809][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:46.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:46.811][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.814][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.818][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.819][private$selectFields]
biodb.TRACE[2024-06-26 21:02:46.820][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 21:02:46.821][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 21:02:46.822][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.822][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.823][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.824][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.825][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.826][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.827][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.828][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.829][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.830][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.831][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-26 21:02:46.832][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.833][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.834][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.835][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.836][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-26 21:02:46.837][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.840][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.844][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:46.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:46.848][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-06-26 21:02:46.849][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-26 21:02:46.850][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-26 21:02:46.867][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-26 21:02:46.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-26 21:02:46.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:46.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-26 21:02:46.874][biodb::testThat]
biodb.INFO [2024-06-26 21:02:46.875][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2024-06-26 21:02:46.876][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:02:46.876][biodb::testThat]
biodb.DEBUG[2024-06-26 21:02:46.878][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-06-26 21:02:46.879][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-26 21:02:46.881][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-06-26 21:02:46.882][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-26 21:02:46.883][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-26 21:02:46.884][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 21:02:46.885][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-26 21:02:46.886][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-26 21:02:46.887][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-26 21:02:46.889][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:46.890][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:46.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:46.895][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:46.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:46.897][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:46.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:46.899][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-06-26 21:02:46.902][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:46.903][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:46.904][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-06-26 21:02:47.298][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-06-26 21:02:47.711][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:47.715][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-06-26 21:02:47.723][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-06-26 21:02:47.728][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-06-26 21:02:47.731][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-26 21:02:47.734][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-26 21:02:47.737][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-26 21:02:47.740][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:47.742][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:47.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:47.753][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:47.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:47.757][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:47.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:47.762][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:47.764][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:47.766][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:47.767][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:47.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:47.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:47.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:47.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:47.785][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:47.786][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:47.787][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:47.788][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:47.790][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:47.791][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:47.792][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:47.793][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:47.794][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:47.796][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:47.797][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:47.798][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:47.799][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:47.800][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:47.801][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:47.802][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:47.803][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:47.804][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:47.805][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:47.806][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:47.807][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:47.808][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:47.809][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:47.810][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:47.811][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:47.812][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:47.813][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:47.814][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:47.815][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:47.816][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:47.817][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:47.818][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:47.819][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:47.820][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:47.821][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:47.822][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:47.823][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:47.824][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:47.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:47.826][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:47.827][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:47.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:47.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:47.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:47.831][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:47.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:47.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:47.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:47.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:47.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:47.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:47.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:47.838][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:47.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:47.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:47.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:47.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:47.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:47.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:47.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:47.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:47.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:47.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:47.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:47.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:47.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:47.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:47.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:47.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:47.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:47.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:47.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:47.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:47.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:47.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:47.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:47.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:47.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:47.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:47.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:47.864][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-06-26 21:02:47.865][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-06-26 21:02:47.872][biodb::testThat]
biodb.INFO [2024-06-26 21:02:47.873][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-06-26 21:02:47.874][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:02:47.875][biodb::testThat]
biodb.DEBUG[2024-06-26 21:02:47.883][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-06-26 21:02:47.884][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-06-26 21:02:47.885][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-06-26 21:02:47.887][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-06-26 21:02:47.888][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2024-06-26 21:02:47.889][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-26 21:02:47.890][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 21:02:47.891][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-26 21:02:47.892][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-26 21:02:47.893][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-26 21:02:47.896][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:47.897][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:47.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:47.902][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:47.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:47.904][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:47.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:47.906][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2024-06-26 21:02:47.909][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:47.910][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:47.911][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-06-26 21:02:48.299][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-06-26 21:02:48.685][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:48.688][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-06-26 21:02:48.691][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-06-26 21:02:48.692][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:48.693][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:48.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:48.698][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:48.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:48.700][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:48.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:48.702][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2024-06-26 21:02:48.704][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:48.705][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:48.707][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2024-06-26 21:02:49.106][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2024-06-26 21:02:49.493][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:49.495][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2024-06-26 21:02:49.509][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2024-06-26 21:02:49.510][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:49.511][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:49.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:49.516][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:49.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:49.518][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:49.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:49.520][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2024-06-26 21:02:49.522][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:49.523][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:49.525][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-06-26 21:02:49.912][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2024-06-26 21:02:50.327][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:50.330][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-06-26 21:02:50.334][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-06-26 21:02:50.338][private$doSaveContentToFile] Saving to cache [3]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2024-06-26 21:02:50.340][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-26 21:02:50.342][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-06-26 21:02:50.343][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-06-26 21:02:50.346][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:50.347][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:50.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:50.355][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:50.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:50.357][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:50.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:50.362][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:50.363][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:50.365][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.366][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:50.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:50.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.373][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:50.375][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:50.376][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.378][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.379][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:50.381][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:50.382][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.384][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.386][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:50.387][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:50.389][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.390][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.391][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:50.392][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:50.393][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.394][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.396][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:50.397][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:50.397][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.398][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.400][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:50.401][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:50.401][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.402][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.404][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:50.405][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:50.406][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.406][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.408][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:50.409][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:50.410][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.410][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.412][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:50.413][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:50.414][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.415][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.416][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:50.417][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:50.418][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.419][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.420][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:50.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:50.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.424][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:50.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:50.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:50.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:50.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.431][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:50.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:50.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:50.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:50.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:50.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:50.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:50.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:50.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:50.447][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:50.448][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:50.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:50.453][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:50.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:50.454][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:50.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:50.457][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:50.458][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:50.459][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.460][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:50.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:50.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.465][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:50.466][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:50.467][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.468][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.469][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:50.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:50.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.473][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:50.474][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:50.475][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.476][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.478][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:50.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:50.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.481][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:50.482][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:50.483][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.484][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.485][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:50.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:50.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.498][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:50.499][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:50.500][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.501][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.502][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:50.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:50.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.506][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:50.507][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:50.508][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.509][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.510][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:50.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:50.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.514][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:50.515][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:50.516][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.517][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.518][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:50.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:50.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.522][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:50.524][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:50.524][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.525][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.527][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:50.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:50.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.531][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:50.532][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:50.532][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.533][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.535][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:50.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:50.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.539][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:50.540][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:50.541][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.542][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.543][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:50.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:50.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.547][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:50.548][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:50.549][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.550][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.551][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:50.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:50.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.555][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:50.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:50.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.559][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:50.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:50.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:50.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:50.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.567][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:50.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:50.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:50.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:50.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:50.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:50.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:50.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:50.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:50.582][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:50.583][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:50.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:50.588][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:50.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:50.590][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:50.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:02:50.593][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:50.594][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:50.595][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.596][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:50.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:50.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.601][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:50.602][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:50.603][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.604][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.605][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:02:50.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:02:50.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.609][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:50.610][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:50.611][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.612][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.613][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:02:50.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:02:50.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.617][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:50.618][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:50.619][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.620][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.622][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:02:50.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:02:50.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.625][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:50.627][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:50.627][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.628][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.630][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:02:50.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:02:50.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.634][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:50.635][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:50.636][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.636][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.638][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:50.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:02:50.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.642][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:50.643][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:50.644][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.645][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.646][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:02:50.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:02:50.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.650][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:50.651][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:50.652][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.653][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.654][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:50.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:50.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.658][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:50.659][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:50.665][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.666][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.668][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:50.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:50.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.672][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:50.673][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:50.674][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.675][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.676][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:02:50.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:02:50.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.680][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:50.681][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:50.682][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.683][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.684][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:02:50.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:02:50.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.688][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:50.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:50.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.692][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:50.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:50.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:50.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:50.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.700][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:02:50.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:02:50.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:50.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:50.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:50.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:50.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:50.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:50.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:50.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:50.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:50.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:50.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:50.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:50.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:50.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:50.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:50.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:50.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:50.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:50.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:50.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:50.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:50.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:50.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:50.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:02:50.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:02:50.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:50.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:02:50.751][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-06-26 21:02:50.752][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-06-26 21:02:50.752][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-06-26 21:02:50.764][biodb::testThat]
biodb.INFO [2024-06-26 21:02:50.766][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2024-06-26 21:02:50.767][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:02:50.767][biodb::testThat]
biodb.INFO [2024-06-26 21:02:50.790][biodb::testThat]
biodb.INFO [2024-06-26 21:02:50.791][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2024-06-26 21:02:50.792][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:02:50.793][biodb::testThat]
biodb.INFO [2024-06-26 21:02:50.800][biodb::testThat]
biodb.INFO [2024-06-26 21:02:50.801][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2024-06-26 21:02:50.802][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:02:50.803][biodb::testThat]
biodb.DEBUG[2024-06-26 21:02:50.806][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[2024-06-26 21:02:50.809][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:50.810][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:50.812][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2024-06-26 21:02:51.264][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2024-06-26 21:02:51.790][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:51.793][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-06-26 21:02:51.796][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-06-26 21:02:51.816][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:02:51.818][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:02:51.819][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:51.820][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:02:51.820][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:51.822][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:02:51.822][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:02:51.823][ef$get] fields variable is a list.
biodb.INFO [2024-06-26 21:02:51.825][biodb::testThat]
biodb.INFO [2024-06-26 21:02:51.826][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2024-06-26 21:02:51.827][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:02:51.828][biodb::testThat]
biodb.ERROR[2024-06-26 21:02:51.841][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-06-26 21:02:51.857][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-06-26 21:02:51.870][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-26 21:02:51.871][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-06-26 21:02:51.873][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-06-26 21:02:51.873][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-26 21:02:51.874][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:51.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:51.876][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:51.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:51.878][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:51.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-26 21:02:51.888][biodb::testContext]
biodb.INFO [2024-06-26 21:02:51.889][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-26 21:02:51.890][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-06-26 21:02:51.891][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-26 21:02:51.892][biodb::testContext]
biodb.INFO [2024-06-26 21:02:51.895][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-26 21:02:51.896][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-06-26 21:02:51.900][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-26 21:02:51.901][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-26 21:02:51.902][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-26 21:02:51.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:51.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:51.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:51.906][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-26 21:02:51.907][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-26 21:02:51.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:51.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:51.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:51.910][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-26 21:02:51.911][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-26 21:02:51.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:51.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:51.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:51.915][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-26 21:02:51.916][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-26 21:02:51.917][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-26 21:02:51.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:51.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:51.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:51.920][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-26 21:02:51.921][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-26 21:02:51.922][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-26 21:02:51.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:51.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:51.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:51.926][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-26 21:02:51.927][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-26 21:02:51.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:51.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:51.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:51.930][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-26 21:02:51.931][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-26 21:02:51.932][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-26 21:02:51.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:51.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:51.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:51.936][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-26 21:02:51.937][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-26 21:02:51.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:51.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:51.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:51.940][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-26 21:02:51.941][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-26 21:02:51.942][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-26 21:02:51.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:51.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:51.945][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[2024-06-26 21:02:51.946][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-26 21:02:51.947][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-26 21:02:51.948][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-26 21:02:51.949][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-26 21:02:51.950][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-26 21:02:51.951][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-26 21:02:51.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:51.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:51.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:51.954][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-26 21:02:51.955][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-26 21:02:51.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:51.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:51.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:51.959][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-26 21:02:51.960][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-26 21:02:51.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:51.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:51.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:51.963][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-26 21:02:51.964][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-26 21:02:51.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:51.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:51.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:51.968][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-26 21:02:51.969][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-26 21:02:51.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:51.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:51.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:51.979][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-26 21:02:51.980][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-26 21:02:51.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:51.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:51.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:51.984][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-26 21:02:51.985][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-26 21:02:51.989][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-26 21:02:51.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:51.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:51.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:51.993][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-26 21:02:51.994][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-26 21:02:51.995][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-26 21:02:51.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:51.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:51.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:51.999][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-26 21:02:52.001][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:52.002][self$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[2024-06-26 21:02:52.003][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:52.004][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:02:52.005][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:52.006][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:02:52.007][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:52.008][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 21:02:52.009][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-26 21:02:52.010][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:02:52.011][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:52.012][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-26 21:02:52.013][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:02:52.014][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:52.015][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:52.016][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-26 21:02:52.016][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-26 21:02:52.016][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-26 21:02:52.016][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-26 21:02:52.016][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-26 21:02:52.017][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 21:02:52.018][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:52.019][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:52.020][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:02:52.021][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:52.022][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:52.023][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:02:52.024][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:52.024][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:02:52.025][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:02:52.026][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:52.027][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:52.028][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-26 21:02:52.030][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:52.031][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-26 21:02:52.032][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:52.033][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:02:52.034][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:52.035][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:02:52.036][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:52.037][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 21:02:52.038][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-26 21:02:52.039][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:02:52.040][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:52.041][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-26 21:02:52.042][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:02:52.043][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:52.044][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:52.045][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-26 21:02:52.045][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-26 21:02:52.045][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-26 21:02:52.045][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-26 21:02:52.045][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-26 21:02:52.046][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 21:02:52.047][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:52.048][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:52.049][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:02:52.050][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:52.051][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:52.051][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:02:52.052][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:52.053][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:02:52.054][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:02:52.055][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:52.056][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:52.057][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-26 21:02:52.059][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:52.060][self$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[2024-06-26 21:02:52.061][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:52.062][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:02:52.063][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:52.064][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:02:52.065][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:52.066][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 21:02:52.067][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-26 21:02:52.068][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:02:52.069][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:52.070][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-26 21:02:52.071][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:02:52.072][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:52.073][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:52.074][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:52.075][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 21:02:52.076][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:52.076][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:52.077][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:02:52.078][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:52.079][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:52.080][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:02:52.081][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:52.082][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:02:52.083][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:02:52.084][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:52.085][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:52.086][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-26 21:02:52.087][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:52.088][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-26 21:02:52.089][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:52.090][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:02:52.091][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:52.092][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:02:52.093][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:52.094][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 21:02:52.095][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-26 21:02:52.096][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:02:52.097][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:52.098][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-26 21:02:52.099][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:02:52.100][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:52.101][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:52.102][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:52.103][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 21:02:52.104][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:52.105][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:52.106][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:02:52.107][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:52.108][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:52.109][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:02:52.110][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:52.111][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:02:52.111][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:02:52.112][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:52.113][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:52.115][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-26 21:02:52.115][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:52.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:52.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:52.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:52.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:52.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:52.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:52.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:52.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:52.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:52.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.323][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[2024-06-26 21:02:52.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:52.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.328][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[2024-06-26 21:02:52.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:52.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.332][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[2024-06-26 21:02:52.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:52.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.336][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.DEBUG[2024-06-26 21:02:52.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:52.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:52.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:52.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:52.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:52.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.348][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[2024-06-26 21:02:52.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:52.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:52.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:52.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:52.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:52.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.361][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[2024-06-26 21:02:52.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:52.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.365][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[2024-06-26 21:02:52.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:52.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:52.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:52.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:52.374][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-26 21:02:52.375][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-26 21:02:52.377][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-26 21:02:52.378][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-26 21:02:52.379][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-26 21:02:52.381][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-26 21:02:52.382][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-26 21:02:52.383][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-26 21:02:52.385][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-26 21:02:52.386][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-26 21:02:52.387][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-26 21:02:52.388][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-26 21:02:52.390][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-26 21:02:52.391][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-26 21:02:52.392][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-26 21:02:52.393][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-26 21:02:52.395][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-26 21:02:52.396][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-26 21:02:52.397][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-26 21:02:52.399][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-26 21:02:52.400][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-26 21:02:52.401][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-26 21:02:52.403][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-26 21:02:52.404][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-26 21:02:52.405][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-26 21:02:52.406][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-26 21:02:52.408][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-26 21:02:52.409][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-26 21:02:52.410][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-26 21:02:52.412][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-26 21:02:52.413][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-26 21:02:52.414][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-26 21:02:52.415][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-26 21:02:52.417][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-26 21:02:52.418][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-26 21:02:52.419][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-26 21:02:52.421][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-26 21:02:52.422][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-26 21:02:52.423][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-26 21:02:52.424][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-26 21:02:52.426][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-26 21:02:52.427][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-26 21:02:52.428][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-26 21:02:52.430][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-26 21:02:52.431][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-26 21:02:52.432][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-26 21:02:52.434][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-26 21:02:52.435][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-26 21:02:52.436][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-26 21:02:52.438][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-26 21:02:52.439][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-26 21:02:52.440][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-26 21:02:52.441][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-26 21:02:52.443][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-26 21:02:52.444][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-26 21:02:52.445][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-26 21:02:52.447][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-26 21:02:52.448][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-26 21:02:52.450][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-26 21:02:52.451][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-26 21:02:52.452][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-26 21:02:52.454][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-26 21:02:52.455][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-26 21:02:52.456][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-26 21:02:52.458][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-26 21:02:52.459][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-26 21:02:52.460][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-26 21:02:52.462][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-26 21:02:52.463][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-26 21:02:52.464][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-26 21:02:52.466][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-26 21:02:52.467][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-26 21:02:52.468][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-26 21:02:52.470][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-26 21:02:52.471][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-26 21:02:52.472][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-26 21:02:52.473][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-26 21:02:52.475][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-26 21:02:52.476][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-26 21:02:52.482][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-26 21:02:52.483][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-26 21:02:52.484][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-26 21:02:52.486][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-26 21:02:52.487][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-26 21:02:52.488][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-26 21:02:52.489][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-26 21:02:52.490][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.492][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:52.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:52.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:52.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:52.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:52.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:52.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:52.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:52.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:52.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:52.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:52.507][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:52.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:52.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:52.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:52.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:52.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:52.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:52.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:52.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:52.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:52.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:52.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:52.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:52.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:52.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:52.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:52.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:52.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:52.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:52.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:52.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:52.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:52.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:52.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:52.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:52.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:52.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:52.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:52.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:52.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.551][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[2024-06-26 21:02:52.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:52.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:52.553][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:52.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:52.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:52.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:52.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:52.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.562][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[2024-06-26 21:02:52.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:52.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:52.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:52.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.568][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[2024-06-26 21:02:52.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:52.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:52.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:52.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.574][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[2024-06-26 21:02:52.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:52.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:52.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:52.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:52.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:52.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:52.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:52.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.585][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[2024-06-26 21:02:52.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:52.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:52.588][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:52.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:52.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:52.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:52.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:52.593][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-06-26 21:02:52.594][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-06-26 21:02:52.596][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:52.597][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-26 21:02:52.598][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:52.599][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:02:52.600][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:52.601][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:02:52.602][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:52.603][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-06-26 21:02:52.604][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-26 21:02:52.605][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:02:52.606][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:52.607][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-06-26 21:02:52.608][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:02:52.609][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-06-26 21:02:52.609][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-06-26 21:02:52.609][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-06-26 21:02:52.609][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-06-26 21:02:52.609][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-06-26 21:02:52.609][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-06-26 21:02:52.609][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-06-26 21:02:52.609][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-06-26 21:02:52.609][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-06-26 21:02:52.609][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-06-26 21:02:52.609][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-06-26 21:02:52.610][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:52.611][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-26 21:02:52.611][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-26 21:02:52.611][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-26 21:02:52.612][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-26 21:02:52.613][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:52.613][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:52.614][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:02:52.615][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:52.616][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:52.617][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:02:52.618][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-26 21:02:52.618][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-06-26 21:02:52.619][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:02:52.620][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:02:52.621][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:52.622][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-06-26 21:02:52.622][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-06-26 21:02:52.623][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-26 21:02:52.624][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-26 21:02:52.626][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-06-26 21:02:52.627][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-26 21:02:52.629][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-26 21:02:52.630][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-26 21:02:52.633][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-06-26 21:02:52.634][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-06-26 21:02:52.635][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-06-26 21:02:52.637][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-06-26 21:02:52.642][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-26 21:02:52.643][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-26 21:02:52.644][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-06-26 21:02:52.645][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-06-26 21:02:52.646][biodb::testThat]
biodb.INFO [2024-06-26 21:02:52.647][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2024-06-26 21:02:52.648][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:02:52.649][biodb::testThat]
biodb.DEBUG[2024-06-26 21:02:52.652][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-06-26 21:02:52.656][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:52.656][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:52.658][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2024-06-26 21:02:53.076][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2024-06-26 21:02:53.668][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:53.671][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2024-06-26 21:02:53.676][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2024-06-26 21:02:53.681][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[2024-06-26 21:02:53.686][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:53.687][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:53.689][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-06-26 21:02:54.157][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-06-26 21:02:54.594][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:54.597][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2024-06-26 21:02:54.603][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2024-06-26 21:02:54.606][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:54.607][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:54.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:54.614][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:54.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:54.617][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:54.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:54.621][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-26 21:02:54.625][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:54.627][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:54.629][private$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[2024-06-26 21:02:55.028][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[2024-06-26 21:02:55.462][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:55.467][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2024-06-26 21:02:55.475][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2024-06-26 21:02:55.480][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:55.482][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:55.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:55.494][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:55.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:55.498][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:55.499][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.DEBUG[2024-06-26 21:02:55.527][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:55.529][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:55.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:55.536][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:55.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:55.538][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:55.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:55.545][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[2024-06-26 21:02:55.548][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-26 21:02:55.550][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-06-26 21:02:55.551][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 21:02:55.553][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-06-26 21:02:55.555][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:55.555][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:55.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:55.561][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:55.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:55.564][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:55.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:55.567][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[2024-06-26 21:02:55.570][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-26 21:02:55.572][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-06-26 21:02:55.573][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 21:02:55.575][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-06-26 21:02:55.577][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:55.578][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:55.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:55.584][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:55.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:55.586][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:55.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:55.588][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:55.589][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:55.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:55.595][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:55.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:55.597][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:55.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:55.602][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[2024-06-26 21:02:55.606][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-26 21:02:55.607][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-06-26 21:02:55.608][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 21:02:55.610][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-06-26 21:02:55.636][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:55.637][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:55.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:55.643][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:55.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:55.645][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:55.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:55.648][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-26 21:02:55.651][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-26 21:02:55.653][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-06-26 21:02:55.654][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 21:02:55.655][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-06-26 21:02:55.657][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:55.658][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:55.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:55.664][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:55.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:55.666][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:55.667][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[2024-06-26 21:02:55.669][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[2024-06-26 21:02:55.672][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:55.673][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:55.675][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-06-26 21:02:56.062][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-06-26 21:02:56.463][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:56.467][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2024-06-26 21:02:56.473][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2024-06-26 21:02:56.476][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:56.478][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:56.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:56.487][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:56.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:56.490][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:56.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-26 21:02:56.501][biodb::testThat]
biodb.INFO [2024-06-26 21:02:56.502][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2024-06-26 21:02:56.504][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:02:56.505][biodb::testThat]
biodb.DEBUG[2024-06-26 21:02:56.510][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-26 21:02:56.515][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:56.517][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:56.520][private$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[2024-06-26 21:02:56.910][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[2024-06-26 21:02:57.319][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:57.325][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-06-26 21:02:57.333][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-06-26 21:02:57.338][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:57.339][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:57.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:57.446][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:57.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:57.451][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:57.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:57.463][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[2024-06-26 21:02:57.471][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:57.474][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:57.479][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-06-26 21:02:57.898][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-06-26 21:02:58.325][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:58.328][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-06-26 21:02:58.332][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-06-26 21:02:58.334][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:02:58.335][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:58.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:58.341][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.343][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-26 21:02:58.350][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-26 21:02:58.351][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-06-26 21:02:58.352][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-06-26 21:02:58.353][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-26 21:02:58.354][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:58.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:58.356][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.358][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-26 21:02:58.364][biodb::testContext]
biodb.INFO [2024-06-26 21:02:58.366][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-26 21:02:58.367][biodb::testContext] Test context - Test web services
biodb.INFO [2024-06-26 21:02:58.368][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-26 21:02:58.369][biodb::testContext]
biodb.INFO [2024-06-26 21:02:58.371][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-26 21:02:58.373][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-06-26 21:02:58.378][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-26 21:02:58.379][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-26 21:02:58.380][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-26 21:02:58.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:58.384][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-26 21:02:58.385][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-26 21:02:58.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:58.389][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-26 21:02:58.390][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-26 21:02:58.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:58.394][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-26 21:02:58.395][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-26 21:02:58.396][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-26 21:02:58.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:58.421][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-26 21:02:58.422][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-26 21:02:58.423][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-26 21:02:58.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:58.427][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-26 21:02:58.428][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-26 21:02:58.429][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:58.432][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-26 21:02:58.433][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-26 21:02:58.434][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-26 21:02:58.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.437][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[2024-06-26 21:02:58.438][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-26 21:02:58.439][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-26 21:02:58.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:58.442][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-26 21:02:58.443][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-26 21:02:58.444][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-26 21:02:58.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.447][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[2024-06-26 21:02:58.448][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-26 21:02:58.449][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-26 21:02:58.450][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-26 21:02:58.451][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-26 21:02:58.452][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-26 21:02:58.453][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-26 21:02:58.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:58.457][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-26 21:02:58.458][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-26 21:02:58.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.460][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[2024-06-26 21:02:58.461][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-26 21:02:58.462][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-26 21:02:58.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:58.466][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-26 21:02:58.467][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-26 21:02:58.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:58.471][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-26 21:02:58.472][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-26 21:02:58.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:58.476][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-26 21:02:58.477][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-26 21:02:58.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:58.480][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-26 21:02:58.481][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-26 21:02:58.484][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-26 21:02:58.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:58.488][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-26 21:02:58.489][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-26 21:02:58.490][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-26 21:02:58.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.492][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[2024-06-26 21:02:58.494][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-26 21:02:58.495][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:58.496][self$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[2024-06-26 21:02:58.497][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:58.498][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:02:58.499][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:58.500][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:02:58.501][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:58.502][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 21:02:58.503][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-26 21:02:58.504][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:02:58.505][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:58.506][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-26 21:02:58.507][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:02:58.508][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:58.509][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:58.510][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-26 21:02:58.510][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-26 21:02:58.510][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-26 21:02:58.510][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-26 21:02:58.510][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-26 21:02:58.511][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 21:02:58.512][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:58.512][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:58.513][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:02:58.514][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:58.515][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:58.516][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:02:58.517][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:58.518][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:02:58.519][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:02:58.519][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:58.520][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:58.521][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-26 21:02:58.523][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:58.524][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-26 21:02:58.525][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:58.526][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:02:58.527][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:58.528][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:02:58.529][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:58.530][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 21:02:58.530][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-26 21:02:58.531][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:02:58.532][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:58.533][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-26 21:02:58.534][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:02:58.535][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:58.536][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:58.537][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-26 21:02:58.537][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-26 21:02:58.537][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-26 21:02:58.537][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-26 21:02:58.537][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-26 21:02:58.538][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 21:02:58.539][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:58.540][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:58.541][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:02:58.541][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:58.542][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:58.543][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:02:58.544][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:58.545][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:02:58.546][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:02:58.547][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:58.548][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:58.549][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-26 21:02:58.551][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:58.552][self$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[2024-06-26 21:02:58.553][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:58.554][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:02:58.555][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:58.556][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:02:58.557][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:58.558][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 21:02:58.559][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-26 21:02:58.560][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:02:58.560][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:58.561][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-26 21:02:58.562][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:02:58.563][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:58.564][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:58.565][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:58.566][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 21:02:58.567][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:58.568][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:58.569][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:02:58.570][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:58.571][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:58.571][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:02:58.572][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:58.573][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:02:58.574][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:02:58.575][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:58.576][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:58.577][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-26 21:02:58.579][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:58.580][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-26 21:02:58.581][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:58.582][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:02:58.587][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:58.588][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:02:58.589][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:58.590][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 21:02:58.591][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-26 21:02:58.592][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:02:58.593][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:58.594][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-26 21:02:58.595][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:02:58.595][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:58.596][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:58.597][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:58.598][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 21:02:58.599][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:58.600][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:58.601][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:02:58.602][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:58.602][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:58.603][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:02:58.604][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:58.605][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:02:58.606][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:02:58.607][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:58.608][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:58.609][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-26 21:02:58.610][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.611][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[2024-06-26 21:02:58.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.615][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[2024-06-26 21:02:58.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.619][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[2024-06-26 21:02:58.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.623][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[2024-06-26 21:02:58.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:58.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:58.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:58.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:58.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:58.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.648][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[2024-06-26 21:02:58.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:58.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:58.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:58.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:58.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:58.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.673][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[2024-06-26 21:02:58.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:58.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:58.682][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-26 21:02:58.684][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-26 21:02:58.685][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-26 21:02:58.686][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-26 21:02:58.688][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-26 21:02:58.689][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-26 21:02:58.690][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-26 21:02:58.691][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-26 21:02:58.693][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-26 21:02:58.694][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-26 21:02:58.695][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-26 21:02:58.697][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-26 21:02:58.698][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-26 21:02:58.699][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-26 21:02:58.700][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-26 21:02:58.702][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-26 21:02:58.703][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-26 21:02:58.704][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-26 21:02:58.706][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-26 21:02:58.707][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-26 21:02:58.708][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-26 21:02:58.710][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-26 21:02:58.711][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-26 21:02:58.713][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-26 21:02:58.714][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-26 21:02:58.715][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-26 21:02:58.717][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-26 21:02:58.718][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-26 21:02:58.719][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-26 21:02:58.721][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-26 21:02:58.722][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-26 21:02:58.724][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-26 21:02:58.725][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-26 21:02:58.726][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-26 21:02:58.728][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-26 21:02:58.729][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-26 21:02:58.730][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-26 21:02:58.732][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-26 21:02:58.733][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-26 21:02:58.735][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-26 21:02:58.736][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-26 21:02:58.737][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-26 21:02:58.739][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-26 21:02:58.745][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-26 21:02:58.746][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-26 21:02:58.748][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-26 21:02:58.749][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-26 21:02:58.750][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-26 21:02:58.752][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-26 21:02:58.753][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-26 21:02:58.754][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-26 21:02:58.756][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-26 21:02:58.757][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-26 21:02:58.758][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-26 21:02:58.759][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-26 21:02:58.761][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-26 21:02:58.762][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-26 21:02:58.763][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-26 21:02:58.765][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-26 21:02:58.766][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-26 21:02:58.767][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-26 21:02:58.769][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-26 21:02:58.770][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-26 21:02:58.771][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-26 21:02:58.773][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-26 21:02:58.774][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-26 21:02:58.776][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-26 21:02:58.777][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-26 21:02:58.778][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-26 21:02:58.780][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-26 21:02:58.781][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-26 21:02:58.782][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-26 21:02:58.783][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-26 21:02:58.785][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-26 21:02:58.786][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-26 21:02:58.787][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-26 21:02:58.789][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-26 21:02:58.790][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-26 21:02:58.791][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-26 21:02:58.792][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-26 21:02:58.794][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-26 21:02:58.795][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-26 21:02:58.796][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-26 21:02:58.798][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-26 21:02:58.799][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-26 21:02:58.800][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-26 21:02:58.801][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.803][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.804][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[2024-06-26 21:02:58.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:58.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:58.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.809][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[2024-06-26 21:02:58.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:58.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:58.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.815][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[2024-06-26 21:02:58.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:58.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:58.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.821][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[2024-06-26 21:02:58.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:58.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:58.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.827][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[2024-06-26 21:02:58.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:58.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:58.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.832][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[2024-06-26 21:02:58.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:58.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:58.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.838][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[2024-06-26 21:02:58.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:58.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:58.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:58.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:58.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:58.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.850][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[2024-06-26 21:02:58.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:58.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:58.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:58.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:58.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:58.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:58.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:58.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:58.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:58.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:58.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:58.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:58.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:58.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:58.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.880][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[2024-06-26 21:02:58.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:58.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:58.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.886][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[2024-06-26 21:02:58.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:58.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:58.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:58.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:58.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:58.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:58.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:58.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:58.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:58.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:58.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:58.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:58.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:58.910][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-06-26 21:02:58.912][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-06-26 21:02:58.914][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:58.915][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-26 21:02:58.916][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:58.916][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:02:58.917][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:58.918][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:02:58.919][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:58.920][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-06-26 21:02:58.921][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-26 21:02:58.922][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:02:58.923][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:58.924][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-06-26 21:02:58.925][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:02:58.926][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-06-26 21:02:58.926][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-06-26 21:02:58.926][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-06-26 21:02:58.926][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-06-26 21:02:58.926][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-06-26 21:02:58.926][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-06-26 21:02:58.926][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-06-26 21:02:58.926][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-06-26 21:02:58.926][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-06-26 21:02:58.926][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-06-26 21:02:58.926][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-06-26 21:02:58.927][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:58.928][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-26 21:02:58.928][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-26 21:02:58.928][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-26 21:02:58.929][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-26 21:02:58.930][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:58.931][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:58.932][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:02:58.933][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:58.933][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:58.934][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:02:58.935][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-26 21:02:58.935][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-06-26 21:02:58.936][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:02:58.937][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:02:58.938][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:58.939][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-06-26 21:02:58.939][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-06-26 21:02:58.940][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-26 21:02:58.942][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-26 21:02:58.943][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-06-26 21:02:58.945][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-26 21:02:58.946][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-26 21:02:58.948][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-26 21:02:58.951][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-06-26 21:02:58.952][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-06-26 21:02:58.953][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-06-26 21:02:58.954][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-06-26 21:02:58.956][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-26 21:02:58.957][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-26 21:02:58.958][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-06-26 21:02:58.959][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-06-26 21:02:58.960][biodb::testThat]
biodb.INFO [2024-06-26 21:02:58.961][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-06-26 21:02:58.962][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:02:58.963][biodb::testThat]
biodb.DEBUG[2024-06-26 21:02:58.966][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-06-26 21:02:58.969][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-26 21:02:58.971][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-06-26 21:02:58.972][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 21:02:58.973][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-06-26 21:02:58.976][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-26 21:02:58.979][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:02:58.980][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:02:58.982][private$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[2024-06-26 21:02:59.372][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[2024-06-26 21:02:59.766][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:02:59.768][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-06-26 21:02:59.772][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-06-26 21:02:59.780][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-26 21:02:59.781][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-06-26 21:02:59.782][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-06-26 21:02:59.783][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-26 21:02:59.784][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:02:59.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:02:59.786][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:02:59.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:02:59.788][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:59.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-26 21:02:59.792][biodb::testContext]
biodb.INFO [2024-06-26 21:02:59.793][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-26 21:02:59.794][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-06-26 21:02:59.795][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-26 21:02:59.796][biodb::testContext]
biodb.INFO [2024-06-26 21:02:59.798][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-26 21:02:59.799][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-06-26 21:02:59.803][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-26 21:02:59.804][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-26 21:02:59.805][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-26 21:02:59.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:59.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:59.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:59.809][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-26 21:02:59.810][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-26 21:02:59.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:59.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:59.812][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.DEBUG[2024-06-26 21:02:59.813][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-26 21:02:59.814][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-26 21:02:59.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:59.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:59.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:59.818][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-26 21:02:59.819][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-26 21:02:59.820][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-26 21:02:59.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:59.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:59.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:59.824][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-26 21:02:59.825][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-26 21:02:59.826][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-26 21:02:59.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:59.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:59.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:59.829][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-26 21:02:59.830][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-26 21:02:59.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:59.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:59.833][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[2024-06-26 21:02:59.834][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-26 21:02:59.835][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-26 21:02:59.836][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-26 21:02:59.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:59.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:59.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:59.840][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-26 21:02:59.841][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-26 21:02:59.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:59.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:59.843][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[2024-06-26 21:02:59.844][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-26 21:02:59.845][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-26 21:02:59.846][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-26 21:02:59.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:59.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:59.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:59.859][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-26 21:02:59.860][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-26 21:02:59.861][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-26 21:02:59.862][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-26 21:02:59.866][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-26 21:02:59.868][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-26 21:02:59.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:59.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:59.871][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[2024-06-26 21:02:59.872][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-26 21:02:59.873][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-26 21:02:59.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:59.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:59.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:59.877][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-26 21:02:59.878][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-26 21:02:59.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:59.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:59.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:59.882][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-26 21:02:59.883][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-26 21:02:59.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:59.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:59.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:59.887][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-26 21:02:59.888][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-26 21:02:59.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:59.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:59.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:59.892][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-26 21:02:59.893][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-26 21:02:59.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:59.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:59.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:59.897][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-26 21:02:59.898][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-26 21:02:59.902][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-26 21:02:59.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:59.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:59.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:59.906][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-26 21:02:59.907][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-26 21:02:59.908][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-26 21:02:59.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:02:59.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:02:59.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:02:59.912][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-26 21:02:59.914][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:59.916][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-26 21:02:59.917][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:59.918][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:02:59.919][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:59.920][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:02:59.921][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:59.922][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 21:02:59.923][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-26 21:02:59.924][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:02:59.925][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:59.926][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-26 21:02:59.927][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:02:59.928][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:59.929][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:59.930][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-26 21:02:59.930][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-26 21:02:59.930][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-26 21:02:59.930][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-26 21:02:59.930][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-26 21:02:59.931][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 21:02:59.932][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:59.933][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:59.934][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:02:59.935][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:59.936][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:59.937][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:02:59.938][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:59.939][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:02:59.940][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:02:59.941][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:59.942][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:59.943][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-26 21:02:59.945][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:59.946][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-26 21:02:59.947][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:59.948][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:02:59.949][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:59.950][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:02:59.951][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:59.953][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 21:02:59.954][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-26 21:02:59.955][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:02:59.956][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:59.957][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-26 21:02:59.958][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:02:59.959][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:59.960][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:59.961][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-26 21:02:59.961][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-26 21:02:59.961][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-26 21:02:59.961][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-26 21:02:59.961][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-26 21:02:59.962][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 21:02:59.963][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:59.964][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:59.965][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:02:59.966][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:59.967][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:59.968][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:02:59.969][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:59.970][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:02:59.971][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:02:59.972][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:59.973][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:59.974][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-26 21:02:59.976][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:59.977][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-26 21:02:59.978][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:59.979][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:02:59.980][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:59.981][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:02:59.982][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:59.983][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 21:02:59.984][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-26 21:02:59.985][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:02:59.986][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:02:59.987][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-26 21:02:59.988][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:02:59.989][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:59.990][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 21:02:59.991][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:02:59.992][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 21:02:59.993][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:59.994][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:59.995][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:02:59.996][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:02:59.997][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:02:59.998][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:02:59.999][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:03:00.000][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:03:00.001][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:03:00.003][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 21:03:00.004][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:03:00.005][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-26 21:03:00.007][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:03:00.008][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-26 21:03:00.009][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:03:00.011][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:03:00.012][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:03:00.013][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:03:00.014][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 21:03:00.015][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 21:03:00.016][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-26 21:03:00.017][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:03:00.018][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:03:00.019][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-26 21:03:00.020][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:03:00.021][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:03:00.022][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 21:03:00.023][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:03:00.024][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 21:03:00.025][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:03:00.026][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:03:00.027][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:03:00.028][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:03:00.029][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:03:00.030][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:03:00.031][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:03:00.032][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:03:00.033][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:03:00.034][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 21:03:00.035][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:03:00.048][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-26 21:03:00.049][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:00.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:00.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:00.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:00.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:00.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:00.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.063][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[2024-06-26 21:03:00.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:00.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:00.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:00.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:00.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:00.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.076][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[2024-06-26 21:03:00.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:00.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:00.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:00.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:00.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:00.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:00.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:00.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:00.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:00.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:00.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:00.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:00.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:00.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:00.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:00.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:00.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:00.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:00.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:00.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:00.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:00.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:00.122][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-26 21:03:00.124][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-26 21:03:00.125][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-26 21:03:00.126][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-26 21:03:00.128][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-26 21:03:00.129][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-26 21:03:00.130][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-26 21:03:00.132][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-26 21:03:00.133][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-26 21:03:00.134][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-26 21:03:00.135][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-26 21:03:00.137][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-26 21:03:00.138][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-26 21:03:00.139][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-26 21:03:00.141][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-26 21:03:00.142][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-26 21:03:00.143][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-26 21:03:00.145][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-26 21:03:00.146][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-26 21:03:00.147][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-26 21:03:00.148][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-26 21:03:00.150][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-26 21:03:00.151][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-26 21:03:00.152][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-26 21:03:00.154][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-26 21:03:00.155][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-26 21:03:00.156][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-26 21:03:00.157][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-26 21:03:00.159][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-26 21:03:00.160][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-26 21:03:00.161][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-26 21:03:00.163][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-26 21:03:00.164][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-26 21:03:00.165][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-26 21:03:00.167][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-26 21:03:00.168][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-26 21:03:00.169][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-26 21:03:00.171][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-26 21:03:00.172][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-26 21:03:00.173][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-26 21:03:00.175][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-26 21:03:00.176][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-26 21:03:00.178][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-26 21:03:00.179][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-26 21:03:00.180][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-26 21:03:00.182][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-26 21:03:00.183][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-26 21:03:00.185][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-26 21:03:00.186][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-26 21:03:00.187][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-26 21:03:00.189][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-26 21:03:00.190][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-26 21:03:00.192][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-26 21:03:00.193][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-26 21:03:00.194][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-26 21:03:00.196][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-26 21:03:00.197][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-26 21:03:00.199][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-26 21:03:00.205][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-26 21:03:00.207][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-26 21:03:00.208][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-26 21:03:00.209][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-26 21:03:00.211][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-26 21:03:00.212][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-26 21:03:00.213][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-26 21:03:00.215][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-26 21:03:00.216][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-26 21:03:00.217][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-26 21:03:00.218][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-26 21:03:00.220][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-26 21:03:00.221][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-26 21:03:00.222][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-26 21:03:00.224][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-26 21:03:00.225][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-26 21:03:00.226][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-26 21:03:00.228][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-26 21:03:00.229][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-26 21:03:00.230][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-26 21:03:00.231][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-26 21:03:00.233][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-26 21:03:00.234][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-26 21:03:00.235][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-26 21:03:00.237][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-26 21:03:00.238][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-26 21:03:00.239][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-26 21:03:00.240][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-26 21:03:00.241][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.243][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:00.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:00.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:00.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:00.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:00.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:00.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:00.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:00.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.255][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[2024-06-26 21:03:00.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:00.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:00.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:00.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.261][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[2024-06-26 21:03:00.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:00.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:00.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:00.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:00.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:00.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:00.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:00.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:00.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:00.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:00.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:00.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:00.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:00.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:00.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:00.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:00.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:00.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:00.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:00.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:00.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:00.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:00.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:00.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:00.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:00.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:00.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:00.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:00.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:00.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:00.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:00.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.309][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[2024-06-26 21:03:00.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:00.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:00.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:00.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:00.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:00.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:00.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:00.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:00.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:00.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:00.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:00.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:00.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:00.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:00.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:00.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.332][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[2024-06-26 21:03:00.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:00.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:00.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:00.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:00.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:00.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:00.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:00.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:00.346][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-06-26 21:03:00.348][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-06-26 21:03:00.349][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:03:00.351][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-26 21:03:00.352][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:03:00.353][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:03:00.354][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:03:00.355][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:03:00.361][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-26 21:03:00.362][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-06-26 21:03:00.363][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-26 21:03:00.364][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:03:00.365][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:03:00.366][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-06-26 21:03:00.367][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:03:00.368][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-06-26 21:03:00.368][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-06-26 21:03:00.368][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-06-26 21:03:00.368][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-06-26 21:03:00.368][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-06-26 21:03:00.368][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-06-26 21:03:00.368][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-06-26 21:03:00.368][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-06-26 21:03:00.368][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-06-26 21:03:00.368][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-06-26 21:03:00.368][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-06-26 21:03:00.369][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-26 21:03:00.370][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-26 21:03:00.370][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-26 21:03:00.370][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-26 21:03:00.371][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-26 21:03:00.372][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:03:00.373][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:03:00.374][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:03:00.375][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:03:00.375][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:03:00.376][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:03:00.377][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-26 21:03:00.377][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-06-26 21:03:00.378][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:03:00.379][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:03:00.380][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-26 21:03:00.381][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-06-26 21:03:00.381][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-06-26 21:03:00.382][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-26 21:03:00.384][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-26 21:03:00.385][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-06-26 21:03:00.387][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-26 21:03:00.388][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-26 21:03:00.389][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-26 21:03:00.393][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-06-26 21:03:00.394][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-06-26 21:03:00.395][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-06-26 21:03:00.397][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-06-26 21:03:00.398][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-26 21:03:00.399][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-26 21:03:00.400][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-06-26 21:03:00.401][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-06-26 21:03:00.402][biodb::testThat]
biodb.INFO [2024-06-26 21:03:00.403][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-06-26 21:03:00.404][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:03:00.405][biodb::testThat]
biodb.DEBUG[2024-06-26 21:03:00.408][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-06-26 21:03:00.412][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-26 21:03:00.413][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-06-26 21:03:00.415][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 21:03:00.416][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-06-26 21:03:00.420][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[2024-06-26 21:03:00.423][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-26 21:03:00.424][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-06-26 21:03:00.426][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 21:03:00.427][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-06-26 21:03:00.431][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-06-26 21:03:00.432][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-26 21:03:00.434][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-06-26 21:03:00.435][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-26 21:03:00.437][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-26 21:03:00.438][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 21:03:00.439][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-26 21:03:00.440][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-26 21:03:00.441][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-26 21:03:00.444][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:03:00.445][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:00.446][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:00.450][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:00.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:00.452][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:00.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:00.454][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-06-26 21:03:00.457][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:03:00.458][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:03:00.459][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-06-26 21:03:00.859][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2024-06-26 21:03:01.892][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:03:01.897][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-06-26 21:03:01.903][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-06-26 21:03:01.907][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-06-26 21:03:01.910][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-26 21:03:01.912][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-26 21:03:01.914][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-26 21:03:01.917][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:03:01.918][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:01.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:01.927][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:01.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:01.930][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:01.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:03:01.937][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:01.938][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:01.940][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:01.941][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:01.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:01.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:01.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:01.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:01.948][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:03:01.949][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:03:01.950][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:01.951][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:01.953][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-26 21:03:01.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-26 21:03:01.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:01.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:01.957][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:03:01.958][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:03:01.959][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:01.960][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:01.962][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:03:01.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:03:01.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:01.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:01.966][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-26 21:03:01.967][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-26 21:03:01.967][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:01.968][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:01.970][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-26 21:03:01.971][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-26 21:03:01.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:01.972][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:01.974][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:03:01.975][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:03:01.976][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:01.977][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:01.978][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:03:01.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:03:01.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:01.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:01.982][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:03:01.983][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:03:01.992][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:01.993][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:01.994][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-26 21:03:01.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:03:01.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:01.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:01.998][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:01.999][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:02.000][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:02.000][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:02.002][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:02.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:02.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:02.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:02.005][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:02.006][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:02.007][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:02.008][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:02.010][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:02.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:02.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:02.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:02.014][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:03:02.014][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:03:02.015][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:02.016][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:02.018][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-26 21:03:02.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-26 21:03:02.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:02.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:02.021][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:03:02.022][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:03:02.023][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:02.024][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:02.025][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-26 21:03:02.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-26 21:03:02.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:02.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:02.029][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:03:02.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:03:02.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:02.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:02.033][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:03:02.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:03:02.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:02.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:02.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:02.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:02.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:02.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:02.040][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:03:02.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:03:02.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:02.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:02.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:02.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:02.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:02.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:02.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:02.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:02.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:02.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:02.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:02.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:02.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:02.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:02.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:02.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:02.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:02.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:02.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:02.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:02.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:02.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:02.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:02.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:02.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:02.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:03:02.065][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-06-26 21:03:02.068][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-26 21:03:02.069][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-06-26 21:03:02.070][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-06-26 21:03:02.071][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-26 21:03:02.072][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:02.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:02.073][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:02.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:02.075][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:02.076][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
>
> proc.time()
user system elapsed
23.696 1.119 60.783
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 0.976 | 0.064 | 2.185 | |
| ChebiEntry | 0.161 | 0.001 | 0.162 | |