Pierrick Roger
| Snapshot Date: 2024-05-30 18:57:37 -0400 (Thu, 30 May 2024) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: devel |
| git_last_commit: dfe3f6c |
| git_last_commit_date: 2024-04-30 11:37:31 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-05-31 19:28:41 -0400 (Fri, 31 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4669 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4404 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4431 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4384 |
| 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 197/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.11.0 (landing page) Pierrick Roger
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | 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 | | ||||||||
|
To the developers/maintainers of the biodbChebi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbChebi.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: biodbChebi |
| Version: 1.11.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings biodbChebi_1.11.0.tar.gz |
| StartedAt: 2024-05-31 01:52:12 -0400 (Fri, 31 May 2024) |
| EndedAt: 2024-05-31 01:54:14 -0400 (Fri, 31 May 2024) |
| EllapsedTime: 122.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbChebi.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings biodbChebi_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.11.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
biodbChebi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘biodbChebi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbChebi)
biodbChebi.Rcheck/tests/testthat.Rout
R version 4.4.0 RC (2024-04-16 r86468) -- "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 [2024-05-31 01:52:57.495][biodb::testContext]
biodb.INFO [2024-05-31 01:52:57.498][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-31 01:52:57.499][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-05-31 01:52:57.500][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-31 01:52:57.501][biodb::testContext]
biodb.INFO [2024-05-31 01:52:57.509][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-05-31 01:52:57.511][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-05-31 01:52:57.520][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-31 01:52:57.521][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-31 01:52:57.522][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-31 01:52:57.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:57.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:57.526][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-31 01:52:57.547][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-31 01:52:57.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:57.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.551][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[2024-05-31 01:52:57.552][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-31 01:52:57.554][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-31 01:52:57.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:57.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:57.558][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-31 01:52:57.559][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-31 01:52:57.560][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-31 01:52:57.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:57.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:57.564][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-31 01:52:57.565][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-31 01:52:57.566][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-31 01:52:57.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:57.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:57.570][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-31 01:52:57.571][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-31 01:52:57.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:57.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.574][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[2024-05-31 01:52:57.575][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-31 01:52:57.576][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-31 01:52:57.577][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-31 01:52:57.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:57.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:57.581][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-31 01:52:57.582][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-31 01:52:57.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:57.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.585][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[2024-05-31 01:52:57.586][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-31 01:52:57.587][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-31 01:52:57.588][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-31 01:52:57.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:57.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:57.592][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-31 01:52:57.593][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-31 01:52:57.594][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-31 01:52:57.595][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-31 01:52:57.596][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-31 01:52:57.597][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-31 01:52:57.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:57.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:57.601][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-31 01:52:57.603][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-31 01:52:57.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:57.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:57.606][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-31 01:52:57.607][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-31 01:52:57.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:57.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:57.611][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-31 01:52:57.612][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-31 01:52:57.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:57.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:57.616][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-31 01:52:57.617][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-31 01:52:57.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:57.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:57.621][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-31 01:52:57.622][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-31 01:52:57.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:57.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:57.626][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-31 01:52:57.627][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-31 01:52:57.630][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-31 01:52:57.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:57.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:57.635][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-31 01:52:57.637][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-31 01:52:57.638][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-31 01:52:57.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:57.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:57.645][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-31 01:52:57.682][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:52:57.718][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-31 01:52:57.719][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:52:57.720][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:52:57.721][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:52:57.722][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:52:57.723][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-31 01:52:57.724][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-31 01:52:57.725][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-31 01:52:57.726][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:52:57.727][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:52:57.728][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-31 01:52:57.729][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:52:57.730][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:52:57.732][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-31 01:52:57.733][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-31 01:52:57.733][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-31 01:52:57.733][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-31 01:52:57.733][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-31 01:52:57.733][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-31 01:52:57.734][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-31 01:52:57.735][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:52:57.736][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:52:57.737][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:52:57.738][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:52:57.739][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:52:57.740][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:52:57.741][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:52:57.742][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:52:57.743][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:52:57.744][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-31 01:52:57.745][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:52:57.746][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-31 01:52:57.748][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:52:57.749][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-31 01:52:57.750][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:52:57.751][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:52:57.752][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:52:57.753][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:52:57.754][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-31 01:52:57.755][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-31 01:52:57.756][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-31 01:52:57.758][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:52:57.759][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:52:57.760][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-31 01:52:57.761][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:52:57.762][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:52:57.763][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-31 01:52:57.764][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-31 01:52:57.764][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-31 01:52:57.764][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-31 01:52:57.764][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-31 01:52:57.764][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-31 01:52:57.765][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-31 01:52:57.766][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:52:57.767][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:52:57.768][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:52:57.769][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:52:57.770][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:52:57.771][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:52:57.772][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:52:57.773][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:52:57.774][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:52:57.775][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-31 01:52:57.776][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:52:57.777][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-31 01:52:57.779][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:52:57.780][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-31 01:52:57.781][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:52:57.782][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:52:57.783][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:52:57.784][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:52:57.785][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-31 01:52:57.786][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-31 01:52:57.787][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-31 01:52:57.789][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:52:57.790][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:52:57.791][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-31 01:52:57.792][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:52:57.793][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:52:57.794][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-31 01:52:57.795][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:52:57.796][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-31 01:52:57.797][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:52:57.798][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:52:57.798][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:52:57.799][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:52:57.800][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:52:57.801][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:52:57.802][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:52:57.803][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:52:57.804][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:52:57.805][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-31 01:52:57.806][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:52:57.808][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-31 01:52:57.809][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:52:57.810][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-31 01:52:57.811][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:52:57.812][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:52:57.813][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:52:57.814][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:52:57.815][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-31 01:52:57.816][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-31 01:52:57.817][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-31 01:52:57.818][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:52:57.820][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:52:57.821][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-31 01:52:57.822][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:52:57.823][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:52:57.824][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-31 01:52:57.825][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:52:57.826][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-31 01:52:57.827][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:52:57.828][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:52:57.829][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:52:57.830][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:52:57.830][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:52:57.831][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:52:57.833][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:52:57.834][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:52:57.834][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:52:57.835][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-31 01:52:57.836][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:52:57.841][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-31 01:52:57.842][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:57.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:57.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:57.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:57.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:57.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:57.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:57.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:57.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:57.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:57.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:57.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:57.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:57.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:57.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:57.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:57.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.862][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[2024-05-31 01:52:57.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:57.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:57.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:57.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.867][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[2024-05-31 01:52:57.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:57.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:57.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:57.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.873][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.DEBUG[2024-05-31 01:52:57.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:57.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:57.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:57.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:57.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:57.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:57.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:57.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:57.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:57.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:57.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:57.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.886][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[2024-05-31 01:52:57.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:57.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:57.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:57.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.891][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[2024-05-31 01:52:57.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:57.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:57.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:57.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:57.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:57.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:57.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:57.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:57.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:57.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:57.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:57.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:57.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:57.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:57.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:57.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.909][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[2024-05-31 01:52:57.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:57.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:57.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:57.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:57.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:57.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:57.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:57.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:57.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:57.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:57.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:57.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:57.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:57.923][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-31 01:52:57.928][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-31 01:52:57.930][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-31 01:52:57.931][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-31 01:52:57.933][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-31 01:52:57.934][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-31 01:52:57.936][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-31 01:52:57.938][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-31 01:52:57.939][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-31 01:52:57.941][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-31 01:52:57.942][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-31 01:52:57.943][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-31 01:52:57.945][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-31 01:52:57.946][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-31 01:52:57.948][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-31 01:52:57.949][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-31 01:52:57.951][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-31 01:52:57.952][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-31 01:52:57.953][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-31 01:52:57.955][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-31 01:52:57.956][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-31 01:52:57.957][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-31 01:52:57.959][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-31 01:52:57.961][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-31 01:52:57.963][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-31 01:52:57.964][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-31 01:52:57.966][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-31 01:52:57.967][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-31 01:52:57.969][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-31 01:52:57.979][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-31 01:52:57.981][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-31 01:52:57.982][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-31 01:52:57.983][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-31 01:52:57.985][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-31 01:52:57.986][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-31 01:52:57.987][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-31 01:52:57.989][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-31 01:52:57.991][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-31 01:52:57.992][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-31 01:52:57.994][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-31 01:52:57.995][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-31 01:52:57.997][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-31 01:52:57.998][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-31 01:52:58.000][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-31 01:52:58.001][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-31 01:52:58.003][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-31 01:52:58.004][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-31 01:52:58.006][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-31 01:52:58.007][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-31 01:52:58.008][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-31 01:52:58.010][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-31 01:52:58.012][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-31 01:52:58.013][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-31 01:52:58.015][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-31 01:52:58.016][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-31 01:52:58.017][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-31 01:52:58.019][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-31 01:52:58.020][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-31 01:52:58.022][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-31 01:52:58.023][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-31 01:52:58.024][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-31 01:52:58.026][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-31 01:52:58.027][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-31 01:52:58.029][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-31 01:52:58.030][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-31 01:52:58.031][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-31 01:52:58.033][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-31 01:52:58.035][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-31 01:52:58.036][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-31 01:52:58.037][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-31 01:52:58.039][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-31 01:52:58.040][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-31 01:52:58.042][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-31 01:52:58.043][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-31 01:52:58.044][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-31 01:52:58.046][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-31 01:52:58.047][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-31 01:52:58.049][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-31 01:52:58.050][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-31 01:52:58.051][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-31 01:52:58.053][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-31 01:52:58.054][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-31 01:52:58.055][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-31 01:52:58.061][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-31 01:52:58.063][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-05-31 01:52:58.066][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-31 01:52:58.067][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:58.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:58.069][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:58.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:58.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:58.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:52:58.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:52:58.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:58.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:58.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:58.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:58.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:58.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:52:58.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:52:58.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:58.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:58.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:58.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:58.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:58.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:52:58.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:52:58.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:58.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:58.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:58.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:58.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:58.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:52:58.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:52:58.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:58.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:58.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:58.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:58.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:58.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:52:58.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:52:58.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:58.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:58.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:58.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:58.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:58.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:52:58.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:52:58.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:58.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:58.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:58.111][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.DEBUG[2024-05-31 01:52:58.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:58.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:52:58.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:52:58.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:58.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:58.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:58.117][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[2024-05-31 01:52:58.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:58.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:52:58.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:52:58.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:58.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:58.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:58.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:58.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:58.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:52:58.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:52:58.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:58.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:58.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:58.129][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[2024-05-31 01:52:58.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:58.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:52:58.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:52:58.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:58.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:58.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:58.134][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[2024-05-31 01:52:58.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:58.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:52:58.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:52:58.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:58.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:58.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:58.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:58.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:58.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:52:58.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:52:58.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:58.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:58.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:58.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:58.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:58.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:52:58.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:52:58.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:58.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:58.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:58.152][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.DEBUG[2024-05-31 01:52:58.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:58.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:52:58.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:52:58.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:58.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:58.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:58.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:58.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:58.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:52:58.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:52:58.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:58.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:58.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:58.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:58.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:58.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:52:58.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:52:58.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:58.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:58.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:58.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:58.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:52:58.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:52:58.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:52:58.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:58.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:58.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:58.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:52:58.177][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-05-31 01:52:58.188][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-05-31 01:52:58.192][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:52:58.194][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-31 01:52:58.195][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:52:58.197][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:52:58.199][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:52:58.200][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:52:58.202][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-31 01:52:58.203][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-05-31 01:52:58.205][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-31 01:52:58.206][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:52:58.207][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:52:58.209][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-05-31 01:52:58.210][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:52:58.212][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-05-31 01:52:58.212][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-05-31 01:52:58.212][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-05-31 01:52:58.212][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-05-31 01:52:58.212][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-05-31 01:52:58.212][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-05-31 01:52:58.212][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-05-31 01:52:58.212][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-05-31 01:52:58.212][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-05-31 01:52:58.212][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-05-31 01:52:58.212][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-05-31 01:52:58.214][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-31 01:52:58.215][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-31 01:52:58.215][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-31 01:52:58.215][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-31 01:52:58.217][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-31 01:52:58.219][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:52:58.221][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:52:58.222][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:52:58.224][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:52:58.225][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:52:58.227][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:52:58.229][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-31 01:52:58.229][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-05-31 01:52:58.231][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:52:58.232][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:52:58.234][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-31 01:52:58.235][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-05-31 01:52:58.235][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-05-31 01:52:58.252][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-31 01:52:58.255][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-31 01:52:58.257][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-05-31 01:52:58.259][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-31 01:52:58.261][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-31 01:52:58.263][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-31 01:52:58.304][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-05-31 01:52:58.307][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-05-31 01:52:58.314][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-05-31 01:52:58.322][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-05-31 01:52:58.332][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-31 01:52:58.334][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-31 01:52:58.337][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-05-31 01:52:58.338][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-05-31 01:52:58.355][biodb::testThat]
biodb.INFO [2024-05-31 01:52:58.357][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-05-31 01:52:58.358][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:52:58.359][biodb::testThat]
biodb.TRACE[2024-05-31 01:52:58.366][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-05-31 01:52:58.368][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-31 01:52:58.375][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-31 01:52:58.390][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:52:58.392][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:52:58.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:52:58.414][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:58.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:58.417][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:58.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:52:58.437][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:52:58.439][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:52:58.441][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.442][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:52:58.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:52:58.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.473][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:52:58.475][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:52:58.476][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.477][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.515][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:52:58.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:52:58.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.520][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:52:58.521][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:52:58.522][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.522][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.524][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:52:58.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:52:58.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.529][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:52:58.531][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:52:58.532][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.533][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.535][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:52:58.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:52:58.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.540][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:52:58.541][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:52:58.542][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.543][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.544][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:52:58.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:52:58.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.548][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:52:58.549][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:52:58.550][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.551][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.552][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:52:58.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:52:58.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.556][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:52:58.557][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:52:58.558][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.559][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.560][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:52:58.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:52:58.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.564][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:52:58.566][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:52:58.567][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.568][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.569][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:52:58.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:52:58.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.573][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:52:58.575][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:52:58.575][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.576][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.579][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:52:58.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:52:58.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.584][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:52:58.586][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:52:58.587][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.589][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.591][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:52:58.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:52:58.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.597][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:52:58.599][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:52:58.600][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.602][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.604][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:52:58.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:52:58.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.609][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:52:58.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:52:58.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.612][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:52:58.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:52:58.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:52:58.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:52:58.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.620][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:52:58.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:52:58.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:52:58.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:52:58.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:52:58.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:52:58.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:52:58.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:52:58.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:52:58.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:52:58.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:52:58.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:52:58.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:52:58.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:52:58.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:52:58.728][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-05-31 01:52:58.732][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:52:58.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:52:58.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.738][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:52:58.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:52:58.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.771][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:52:58.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:52:58.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.776][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:52:58.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:52:58.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.780][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:52:58.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:52:58.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.786][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:52:58.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:52:58.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.792][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-31 01:52:58.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-31 01:52:58.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.798][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-31 01:52:58.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-31 01:52:58.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.805][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-31 01:52:58.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-31 01:52:58.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.811][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-31 01:52:58.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-31 01:52:58.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:52:58.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:52:58.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.863][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:52:58.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:52:58.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:52:58.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:52:58.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:52:58.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:52:58.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:52:58.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:52:58.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:52:58.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:52:58.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:52:58.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:52:58.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:52:58.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:52:58.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.899][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:52:58.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:52:58.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.903][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:52:58.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:52:58.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.907][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:52:58.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:52:58.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:52:58.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:52:58.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:52:58.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:52:58.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:52:58.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:52:58.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.930][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:52:58.931][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:52:58.932][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.964][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:52:58.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:52:58.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.977][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:52:58.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:52:58.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.982][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:52:58.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:52:58.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.986][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:52:58.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:52:58.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.990][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:52:58.991][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:52:58.991][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.992][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:58.993][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:52:58.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:52:58.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:58.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.005][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:52:59.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:52:59.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.009][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:52:59.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:52:59.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.013][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:52:59.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:52:59.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.017][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:52:59.018][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:52:59.019][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.020][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.021][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:52:59.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:52:59.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.032][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:52:59.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:52:59.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.036][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:52:59.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:52:59.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.040][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:52:59.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:52:59.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.044][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:52:59.045][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:52:59.046][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.047][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.048][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:52:59.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:52:59.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:52:59.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:52:59.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.064][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:52:59.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:52:59.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.068][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:52:59.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:52:59.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.072][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:52:59.073][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:52:59.074][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.075][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.076][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:52:59.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:52:59.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.088][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:52:59.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:52:59.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.093][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:52:59.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:52:59.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.097][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:52:59.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:52:59.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.101][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:52:59.103][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:52:59.104][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.105][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.106][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:52:59.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:52:59.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.119][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:52:59.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:52:59.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.124][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:52:59.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:52:59.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.127][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:52:59.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:52:59.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.131][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:52:59.132][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:52:59.133][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.134][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.135][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:52:59.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:52:59.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.146][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-31 01:52:59.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:52:59.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.151][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-31 01:52:59.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:52:59.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.155][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-31 01:52:59.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:52:59.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.159][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-31 01:52:59.160][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:52:59.160][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.161][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.162][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-31 01:52:59.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:52:59.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.174][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:52:59.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:52:59.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.178][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:52:59.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:52:59.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.182][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:52:59.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:52:59.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.186][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:52:59.187][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:52:59.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.194][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.195][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:52:59.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:52:59.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.207][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:52:59.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:52:59.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.211][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:52:59.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:52:59.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.216][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:52:59.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:52:59.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.220][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:52:59.221][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:52:59.222][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.223][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.224][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:52:59.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:52:59.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.235][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:52:59.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:52:59.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.240][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:52:59.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:52:59.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.244][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:52:59.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:52:59.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.248][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:52:59.249][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:52:59.250][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.250][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.251][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:52:59.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:52:59.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.263][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:52:59.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:52:59.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.267][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:52:59.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:52:59.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.271][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:52:59.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:52:59.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.275][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:52:59.276][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:52:59.277][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.277][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.278][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:52:59.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:52:59.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.289][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:52:59.291][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:52:59.292][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.293][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.297][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:52:59.298][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:52:59.299][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.300][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.305][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:52:59.306][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:52:59.307][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.308][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.312][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:52:59.313][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:52:59.314][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.315][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.319][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:52:59.321][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:52:59.322][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.322][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.327][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:52:59.328][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:52:59.329][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.330][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.335][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:52:59.336][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:52:59.337][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.338][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.342][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:52:59.343][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:52:59.344][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.345][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.350][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-31 01:52:59.351][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:52:59.352][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.353][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.358][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:52:59.359][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:52:59.360][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.361][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.365][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:52:59.366][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:52:59.367][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.368][ef$get] fields variable is a list.
biodb.INFO [2024-05-31 01:52:59.376][biodb::testThat]
biodb.INFO [2024-05-31 01:52:59.377][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-05-31 01:52:59.378][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:52:59.379][biodb::testThat]
biodb.DEBUG[2024-05-31 01:52:59.393][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-05-31 01:52:59.400][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-31 01:52:59.405][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-05-31 01:52:59.407][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-31 01:52:59.408][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-05-31 01:52:59.409][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-31 01:52:59.438][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-31 01:52:59.440][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-31 01:52:59.441][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:52:59.442][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:52:59.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:52:59.448][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:52:59.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:52:59.450][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:52:59.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:52:59.453][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:52:59.455][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:52:59.455][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.456][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:52:59.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:52:59.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.478][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:52:59.479][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:52:59.480][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.481][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.483][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:52:59.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:52:59.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.487][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:52:59.488][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:52:59.489][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.489][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.491][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:52:59.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:52:59.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.495][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:52:59.496][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:52:59.497][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.498][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.499][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:52:59.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:52:59.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.503][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:52:59.504][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:52:59.505][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.506][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.507][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:52:59.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:52:59.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.511][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:52:59.512][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:52:59.513][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.514][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.515][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:52:59.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:52:59.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.519][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:52:59.520][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:52:59.521][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.522][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.524][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:52:59.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:52:59.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.528][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:52:59.529][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:52:59.530][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.531][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.532][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:52:59.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:52:59.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.536][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:52:59.537][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:52:59.538][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.539][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.541][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:52:59.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:52:59.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.545][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:52:59.546][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:52:59.547][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.548][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.549][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:52:59.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:52:59.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.553][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:52:59.554][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:52:59.555][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.556][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.558][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:52:59.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:52:59.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.562][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:52:59.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:52:59.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.566][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:52:59.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:52:59.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:52:59.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:52:59.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.573][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:52:59.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:52:59.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:52:59.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:52:59.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:52:59.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:52:59.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:52:59.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:52:59.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:52:59.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:52:59.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:52:59.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:52:59.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:52:59.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:52:59.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:52:59.600][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-05-31 01:52:59.601][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-05-31 01:52:59.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-05-31 01:52:59.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.605][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-05-31 01:52:59.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-05-31 01:52:59.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.609][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-05-31 01:52:59.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-05-31 01:52:59.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-31 01:52:59.619][biodb::testThat]
biodb.INFO [2024-05-31 01:52:59.621][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-05-31 01:52:59.621][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:52:59.622][biodb::testThat]
biodb.TRACE[2024-05-31 01:52:59.626][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:52:59.627][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:52:59.634][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.635][ef$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:52:59.637][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-05-31 01:52:59.663][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:52:59.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:52:59.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.667][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:52:59.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:52:59.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.672][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:52:59.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:52:59.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:52:59.679][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-05-31 01:52:59.683][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-05-31 01:52:59.705][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-31 01:52:59.721][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-05-31 01:52:59.722][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-31 01:52:59.724][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-05-31 01:52:59.747][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[2024-05-31 01:52:59.750][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-31 01:52:59.752][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-31 01:52:59.753][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-31 01:52:59.755][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-05-31 01:52:59.757][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-05-31 01:52:59.768][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:52:59.769][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:52:59.770][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.771][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.772][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:52:59.773][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:52:59.774][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.775][ef$get] fields variable is a list.
biodb.INFO [2024-05-31 01:52:59.780][biodb::testThat]
biodb.INFO [2024-05-31 01:52:59.781][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-05-31 01:52:59.782][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:52:59.783][biodb::testThat]
biodb.TRACE[2024-05-31 01:52:59.806][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:52:59.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:52:59.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.811][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:52:59.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:52:59.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.814][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:52:59.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:52:59.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:52:59.880][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[2024-05-31 01:52:59.883][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-31 01:52:59.885][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-31 01:52:59.886][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-31 01:52:59.887][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-05-31 01:52:59.902][biodb::testThat]
biodb.INFO [2024-05-31 01:52:59.903][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-05-31 01:52:59.904][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:52:59.905][biodb::testThat]
biodb.TRACE[2024-05-31 01:52:59.925][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:52:59.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:52:59.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.929][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:52:59.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:52:59.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.933][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:52:59.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:52:59.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.937][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:52:59.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:52:59.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.940][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:52:59.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:52:59.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.944][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:52:59.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:52:59.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.948][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-31 01:52:59.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-31 01:52:59.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.952][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-31 01:52:59.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-31 01:52:59.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.956][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-31 01:52:59.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-31 01:52:59.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.960][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-31 01:52:59.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-31 01:52:59.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.982][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:52:59.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:52:59.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.986][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:52:59.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:52:59.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.990][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:52:59.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:52:59.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.994][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:52:59.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:52:59.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:52:59.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:52:59.998][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:52:59.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:00.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:00.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:00.002][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:00.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:00.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:00.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:00.006][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-31 01:53:00.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-31 01:53:00.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:00.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:00.009][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-31 01:53:00.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-31 01:53:00.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:00.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:00.013][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-31 01:53:00.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-31 01:53:00.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:00.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:00.017][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-31 01:53:00.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-31 01:53:00.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:00.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-31 01:53:00.027][biodb::testThat]
biodb.INFO [2024-05-31 01:53:00.028][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-05-31 01:53:00.029][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:53:00.030][biodb::testThat]
biodb.INFO [2024-05-31 01:53:00.044][biodb::testThat]
biodb.INFO [2024-05-31 01:53:00.045][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-05-31 01:53:00.046][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:53:00.047][biodb::testThat]
biodb.INFO [2024-05-31 01:53:00.056][biodb::testThat]
biodb.INFO [2024-05-31 01:53:00.057][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-05-31 01:53:00.058][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:53:00.059][biodb::testThat]
biodb.DEBUG[2024-05-31 01:53:00.063][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-05-31 01:53:00.726][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-05-31 01:53:01.840][biodb::testThat]
biodb.INFO [2024-05-31 01:53:01.842][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-05-31 01:53:01.844][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:53:01.845][biodb::testThat]
biodb.DEBUG[2024-05-31 01:53:02.275][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[2024-05-31 01:53:02.748][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:02.751][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:02.753][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:02.755][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:02.757][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:02.758][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:02.760][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:02.762][ef$get] fields variable is a list.
biodb.INFO [2024-05-31 01:53:02.766][biodb::testThat]
biodb.INFO [2024-05-31 01:53:02.768][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2024-05-31 01:53:02.770][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:53:02.772][biodb::testThat]
biodb.TRACE[2024-05-31 01:53:02.789][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:02.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:02.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:02.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:02.795][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:02.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:02.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:02.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:02.800][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:02.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:02.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:02.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:02.925][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[2024-05-31 01:53:02.929][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-31 01:53:02.930][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-31 01:53:02.932][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-31 01:53:02.933][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-05-31 01:53:03.000][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[2024-05-31 01:53:03.004][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-31 01:53:03.005][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-31 01:53:03.006][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-31 01:53:03.008][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-05-31 01:53:03.021][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-31 01:53:03.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-31 01:53:03.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:03.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:03.029][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:03.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:03.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:03.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:03.033][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:03.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:03.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:03.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:03.036][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:03.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:03.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:03.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:03.041][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:03.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:03.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:03.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:03.045][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:03.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:03.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:03.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:03.063][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[2024-05-31 01:53:03.067][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-31 01:53:03.068][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-05-31 01:53:03.070][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-31 01:53:03.072][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-05-31 01:53:03.074][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:03.075][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:03.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:03.082][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:03.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:03.083][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:03.084][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[2024-05-31 01:53:03.085][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-05-31 01:53:03.130][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-31 01:53:03.132][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-05-31 01:53:03.134][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-31 01:53:03.135][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-31 01:53:03.136][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-31 01:53:03.137][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-31 01:53:03.138][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-31 01:53:03.139][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-31 01:53:03.141][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:03.142][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:03.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:03.148][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:03.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:03.150][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:03.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:03.152][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-05-31 01:53:03.155][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:03.155][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:03.157][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-05-31 01:53:03.553][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-05-31 01:53:03.949][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:03.951][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-05-31 01:53:03.965][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-05-31 01:53:03.968][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-05-31 01:53:03.969][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-31 01:53:03.971][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-31 01:53:03.972][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-31 01:53:03.973][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:03.974][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:03.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:03.979][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:03.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:03.981][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:03.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:03.984][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:03.985][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:03.986][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:03.987][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:03.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:03.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:03.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:03.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:03.992][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:03.993][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:03.994][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:03.994][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:03.996][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:03.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:03.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:03.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:03.999][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:04.000][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:04.001][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:04.002][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:04.004][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:04.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:04.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:04.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:04.016][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:04.017][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:04.018][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:04.019][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:04.020][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:04.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:04.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:04.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:04.024][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:04.025][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:04.026][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:04.026][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:04.028][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:04.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:04.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:04.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:04.031][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:04.033][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:04.033][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:04.034][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:04.035][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:04.036][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:04.037][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:04.038][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:04.039][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:04.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:04.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:04.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:04.043][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:04.044][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:04.045][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:04.046][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:04.047][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:04.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:04.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:04.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:04.051][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:04.052][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:04.053][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:04.054][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:04.055][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:04.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:04.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:04.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:04.059][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:04.060][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:04.061][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:04.062][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:04.063][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:04.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:04.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:04.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:04.067][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:04.068][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:04.069][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:04.069][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:04.071][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:04.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:04.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:04.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:04.074][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:04.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:04.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:04.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:04.078][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:04.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:04.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:04.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:04.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:04.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:04.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:04.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:04.086][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:04.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:04.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:04.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:04.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:04.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:04.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:04.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:04.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:04.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:04.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:04.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:04.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:04.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:04.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:04.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:04.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:04.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:04.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:04.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:04.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:04.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:04.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:04.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:04.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:04.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:04.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:04.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:04.111][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-05-31 01:53:04.120][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:04.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:04.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:04.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:04.124][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:04.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:04.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:04.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:04.127][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:04.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:04.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:04.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:04.132][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[2024-05-31 01:53:04.134][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-31 01:53:04.136][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-05-31 01:53:04.137][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-31 01:53:04.138][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-05-31 01:53:04.153][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:04.154][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:04.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:04.159][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:04.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:04.160][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:04.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:04.162][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:04.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:04.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:04.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:04.166][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:04.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:04.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:04.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:04.174][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:04.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:04.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:04.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:04.178][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:04.178][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:04.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:04.183][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:04.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:04.185][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:04.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:04.187][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-05-31 01:53:04.188][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-31 01:53:04.189][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-05-31 01:53:04.190][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-31 01:53:04.191][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-31 01:53:04.192][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-31 01:53:04.193][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-31 01:53:04.194][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-31 01:53:04.195][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-31 01:53:04.208][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:04.209][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:04.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:04.214][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:04.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:04.216][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:04.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:04.218][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-05-31 01:53:04.232][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:04.233][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:04.247][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-05-31 01:53:04.635][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-05-31 01:53:05.027][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:05.030][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-05-31 01:53:05.036][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-05-31 01:53:05.040][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-05-31 01:53:05.043][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-31 01:53:05.045][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-31 01:53:05.047][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-31 01:53:05.050][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:05.052][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:05.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:05.061][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:05.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:05.064][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:05.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:05.069][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:05.071][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:05.073][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.074][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:05.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:05.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:05.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:05.082][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:05.083][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:05.084][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.086][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:05.087][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:05.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:05.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:05.092][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:05.093][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:05.094][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.095][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:05.097][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:05.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:05.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:05.101][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:05.102][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:05.103][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.104][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:05.106][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:05.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:05.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:05.109][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:05.110][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:05.111][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.112][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:05.113][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:05.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:05.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:05.117][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:05.118][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:05.119][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.120][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:05.121][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:05.122][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:05.123][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.124][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:05.125][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:05.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:05.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:05.137][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:05.138][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:05.139][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.140][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:05.141][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:05.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:05.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:05.145][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:05.146][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:05.147][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.148][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:05.149][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:05.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:05.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:05.153][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:05.154][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:05.155][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.156][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:05.157][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:05.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:05.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:05.161][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:05.162][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:05.163][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.164][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:05.165][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:05.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:05.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:05.169][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:05.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:05.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:05.172][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:05.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:05.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:05.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:05.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:05.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:05.180][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:05.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:05.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:05.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:05.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:05.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:05.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:05.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:05.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:05.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:05.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:05.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:05.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:05.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:05.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:05.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:05.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:05.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:05.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:05.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:05.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:05.207][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-05-31 01:53:05.208][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:05.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:05.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:05.212][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:05.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:05.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:05.215][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:05.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:05.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:05.234][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[2024-05-31 01:53:05.237][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-31 01:53:05.239][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-31 01:53:05.240][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-31 01:53:05.241][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-05-31 01:53:05.244][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:05.245][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:05.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:05.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:05.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:05.251][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:05.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:05.253][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:05.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:05.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:05.257][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:05.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:05.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:05.260][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:05.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:05.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:05.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:05.264][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:05.269][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:05.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:05.276][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:05.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:05.278][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:05.279][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[2024-05-31 01:53:05.280][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-05-31 01:53:05.281][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-31 01:53:05.284][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-05-31 01:53:05.285][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-31 01:53:05.286][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-31 01:53:05.287][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-31 01:53:05.288][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-31 01:53:05.290][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-31 01:53:05.290][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-31 01:53:05.294][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:05.295][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:05.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:05.301][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:05.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:05.303][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:05.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:05.306][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-05-31 01:53:05.326][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:05.327][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:05.328][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-05-31 01:53:05.717][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-05-31 01:53:06.108][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:06.111][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-05-31 01:53:06.115][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-05-31 01:53:06.120][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-05-31 01:53:06.122][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-31 01:53:06.124][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-31 01:53:06.126][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-31 01:53:06.128][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:06.129][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:06.130][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:06.138][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:06.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:06.140][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:06.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:06.144][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:06.146][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:06.147][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:06.148][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:06.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:06.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:06.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:06.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:06.155][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:06.156][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:06.157][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:06.159][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:06.160][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:06.162][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:06.163][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:06.164][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:06.166][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:06.167][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:06.168][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:06.169][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:06.171][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:06.172][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:06.173][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:06.174][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:06.176][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:06.177][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:06.178][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:06.179][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:06.181][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:06.182][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:06.183][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:06.184][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:06.186][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:06.187][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:06.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:06.190][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:06.191][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:06.192][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:06.193][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:06.195][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:06.196][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:06.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:06.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:06.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:06.201][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:06.203][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:06.204][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:06.205][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:06.207][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:06.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:06.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:06.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:06.211][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:06.213][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:06.214][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:06.215][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:06.217][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:06.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:06.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:06.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:06.222][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:06.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:06.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:06.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:06.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:06.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:06.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:06.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:06.231][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:06.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:06.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:06.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:06.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:06.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:06.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:06.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:06.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:06.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:06.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:06.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:06.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:06.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:06.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:06.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:06.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:06.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:06.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:06.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:06.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:06.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:06.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:06.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:06.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:06.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:06.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:06.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:06.266][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-05-31 01:53:06.267][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:06.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:06.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:06.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:06.272][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:06.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:06.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:06.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:06.277][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:06.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:06.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:06.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:06.282][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:06.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:06.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:06.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:06.286][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:06.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:06.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:06.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:06.292][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:06.293][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:06.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:06.299][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:06.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:06.301][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:06.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:06.303][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-05-31 01:53:06.305][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-31 01:53:06.306][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-05-31 01:53:06.308][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-31 01:53:06.309][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-31 01:53:06.310][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-31 01:53:06.312][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-31 01:53:06.313][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-31 01:53:06.314][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-31 01:53:06.327][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:06.328][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:06.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:06.335][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:06.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:06.337][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:06.338][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[2024-05-31 01:53:06.339][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-05-31 01:53:06.342][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:06.343][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:06.345][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-05-31 01:53:06.852][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-05-31 01:53:07.240][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:07.243][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-05-31 01:53:07.246][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-05-31 01:53:07.249][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-05-31 01:53:07.251][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-31 01:53:07.252][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-31 01:53:07.253][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-31 01:53:07.255][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:07.256][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:07.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:07.262][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:07.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:07.263][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:07.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:07.267][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:07.268][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:07.269][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:07.270][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:07.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:07.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:07.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:07.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:07.275][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:07.276][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:07.277][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:07.278][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:07.280][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:07.281][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:07.282][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:07.282][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:07.284][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:07.285][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:07.286][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:07.287][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:07.288][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:07.289][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:07.290][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:07.291][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:07.293][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:07.294][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:07.294][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:07.295][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:07.297][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:07.298][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:07.299][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:07.300][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:07.301][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:07.302][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:07.303][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:07.304][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:07.305][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:07.306][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:07.307][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:07.308][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:07.309][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:07.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:07.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:07.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:07.313][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:07.314][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:07.315][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:07.316][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:07.317][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:07.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:07.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:07.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:07.321][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:07.322][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:07.323][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:07.324][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:07.325][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:07.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:07.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:07.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:07.329][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:07.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:07.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:07.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:07.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:07.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:07.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:07.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:07.336][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:07.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:07.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:07.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:07.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:07.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:07.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:07.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:07.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:07.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:07.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:07.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:07.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:07.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:07.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:07.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:07.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:07.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:07.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:07.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:07.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:07.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:07.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:07.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:07.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:07.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:07.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:07.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:07.364][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-05-31 01:53:07.365][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:07.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:07.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:07.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:07.369][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:07.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:07.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:07.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:07.373][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:07.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:07.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:07.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:07.377][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:07.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:07.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:07.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:07.382][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:07.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:07.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:07.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:07.386][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:07.387][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:07.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:07.393][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:07.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:07.406][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:07.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:07.408][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-05-31 01:53:07.409][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-31 01:53:07.411][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-05-31 01:53:07.412][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-31 01:53:07.413][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-31 01:53:07.414][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-31 01:53:07.415][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-31 01:53:07.416][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-31 01:53:07.417][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-31 01:53:07.420][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:07.421][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:07.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:07.427][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:07.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:07.429][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:07.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:07.431][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-05-31 01:53:07.434][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:07.435][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:07.437][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-05-31 01:53:07.828][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-05-31 01:53:08.245][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:08.248][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-05-31 01:53:08.251][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-05-31 01:53:08.254][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-05-31 01:53:08.255][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-31 01:53:08.256][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-31 01:53:08.257][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-31 01:53:08.259][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:08.260][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:08.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:08.266][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:08.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:08.267][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:08.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:08.271][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:08.272][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:08.273][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:08.274][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:08.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:08.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:08.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:08.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:08.279][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:08.280][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:08.281][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:08.282][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:08.283][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:08.284][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:08.285][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:08.286][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:08.287][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:08.288][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:08.289][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:08.290][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:08.292][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:08.293][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:08.294][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:08.294][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:08.296][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:08.297][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:08.298][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:08.298][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:08.300][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:08.301][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:08.302][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:08.303][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:08.304][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:08.305][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:08.306][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:08.307][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:08.308][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:08.309][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:08.310][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:08.311][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:08.312][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:08.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:08.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:08.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:08.316][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:08.317][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:08.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:08.319][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:08.321][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:08.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:08.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:08.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:08.324][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:08.325][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:08.326][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:08.327][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:08.329][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:08.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:08.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:08.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:08.333][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:08.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:08.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:08.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:08.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:08.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:08.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:08.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:08.340][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:08.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:08.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:08.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:08.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:08.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:08.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:08.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:08.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:08.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:08.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:08.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:08.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:08.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:08.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:08.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:08.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:08.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:08.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:08.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:08.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:08.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:08.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:08.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:08.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:08.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:08.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:08.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:08.368][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-05-31 01:53:08.369][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:08.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:08.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:08.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:08.373][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:08.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:08.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:08.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:08.377][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:08.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:08.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:08.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:08.381][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:08.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:08.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:08.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:08.396][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:08.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:08.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:08.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:08.400][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:08.401][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:08.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:08.407][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:08.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:08.409][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:08.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:08.411][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-05-31 01:53:08.412][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-31 01:53:08.413][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-05-31 01:53:08.414][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-31 01:53:08.415][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-31 01:53:08.417][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-31 01:53:08.418][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-31 01:53:08.419][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-31 01:53:08.420][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-31 01:53:08.422][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:08.423][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:08.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:08.429][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:08.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:08.430][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:08.431][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[2024-05-31 01:53:08.432][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-05-31 01:53:08.435][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:08.436][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:08.437][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-05-31 01:53:08.827][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-05-31 01:53:09.246][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2024-05-31 01:53:09.249][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-05-31 01:53:09.251][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-05-31 01:53:09.255][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-05-31 01:53:09.257][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-05-31 01:53:09.259][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-31 01:53:09.260][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-31 01:53:09.261][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-31 01:53:09.263][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:09.264][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:09.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:09.271][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:09.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:09.273][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:09.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:09.277][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:09.278][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:09.279][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.280][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:09.282][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:09.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:09.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:09.286][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:09.287][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:09.288][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.289][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:09.291][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:09.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:09.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:09.295][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:09.296][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:09.297][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.298][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:09.299][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:09.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:09.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:09.303][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:09.304][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:09.305][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.306][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:09.308][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:09.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:09.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:09.312][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:09.313][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:09.314][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.315][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:09.316][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:09.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:09.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:09.320][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:09.321][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:09.322][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.323][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:09.325][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:09.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:09.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:09.329][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:09.330][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:09.331][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.332][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:09.333][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:09.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:09.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:09.337][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:09.338][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:09.339][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.340][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:09.341][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:09.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:09.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:09.345][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:09.346][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:09.347][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.348][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:09.350][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:09.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:09.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:09.354][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:09.355][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:09.356][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.357][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:09.358][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:09.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:09.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:09.363][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:09.364][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:09.365][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.366][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:09.367][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:09.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:09.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:09.371][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:09.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:09.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:09.375][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:09.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:09.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:09.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:09.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:09.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:09.400][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:09.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:09.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:09.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:09.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:09.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:09.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:09.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:09.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:09.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:09.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:09.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:09.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:09.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:09.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:09.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:09.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:09.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:09.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:09.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:09.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:09.429][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-05-31 01:53:09.430][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:09.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:09.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:09.434][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:09.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:09.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:09.438][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:09.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:09.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:09.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:09.441][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:09.442][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:09.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:09.447][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:09.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:09.449][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:09.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:09.451][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-05-31 01:53:09.452][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-31 01:53:09.453][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-05-31 01:53:09.454][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-31 01:53:09.455][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-31 01:53:09.456][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-31 01:53:09.457][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-31 01:53:09.458][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-31 01:53:09.459][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-31 01:53:09.461][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:09.462][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:09.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:09.467][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:09.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:09.469][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:09.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:09.471][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-05-31 01:53:09.473][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:09.474][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:09.475][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-05-31 01:53:09.881][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-05-31 01:53:10.316][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:10.319][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-05-31 01:53:10.323][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-05-31 01:53:10.326][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-05-31 01:53:10.327][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-31 01:53:10.329][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-31 01:53:10.330][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-31 01:53:10.332][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:10.333][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:10.334][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:10.339][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:10.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:10.341][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:10.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:10.345][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:10.346][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:10.347][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.348][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:10.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:10.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:10.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:10.354][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:10.355][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:10.356][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.357][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:10.359][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:10.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:10.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:10.363][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:10.364][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:10.365][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.366][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:10.368][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:10.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:10.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:10.372][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:10.373][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:10.374][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.375][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:10.377][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:10.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:10.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:10.381][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:10.382][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:10.382][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.383][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:10.385][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:10.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:10.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:10.389][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:10.390][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:10.391][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.392][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:10.393][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:10.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:10.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:10.397][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:10.398][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:10.399][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.400][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:10.401][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:10.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:10.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:10.405][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:10.411][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:10.417][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.418][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:10.419][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:10.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:10.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:10.423][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:10.424][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:10.425][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.426][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:10.427][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:10.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:10.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:10.431][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:10.432][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:10.433][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.434][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:10.435][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:10.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:10.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:10.439][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:10.440][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:10.441][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.442][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:10.443][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:10.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:10.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:10.447][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:10.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:10.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:10.451][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:10.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:10.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:10.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:10.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:10.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:10.459][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:10.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:10.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:10.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:10.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:10.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:10.467][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:10.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:10.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:10.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:10.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:10.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:10.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:10.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:10.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:10.480][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:10.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:10.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:10.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:10.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:10.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:10.488][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-05-31 01:53:10.489][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:10.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:10.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:10.493][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:10.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:10.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:10.497][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:10.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:10.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:10.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:10.501][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:10.502][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:10.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:10.507][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:10.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:10.509][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:10.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:10.511][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-05-31 01:53:10.512][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-31 01:53:10.514][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-05-31 01:53:10.515][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-31 01:53:10.516][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-31 01:53:10.517][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-31 01:53:10.518][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-31 01:53:10.519][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-31 01:53:10.520][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-31 01:53:10.523][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:10.524][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:10.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:10.530][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:10.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:10.532][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:10.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:10.534][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-05-31 01:53:10.537][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:10.538][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:10.540][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-05-31 01:53:10.931][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-05-31 01:53:11.374][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2024-05-31 01:53:11.377][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-05-31 01:53:11.380][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-05-31 01:53:11.386][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-05-31 01:53:11.391][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-05-31 01:53:11.393][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-31 01:53:11.395][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-31 01:53:11.397][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-31 01:53:11.400][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:11.402][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:11.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:11.412][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:11.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:11.415][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:11.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:11.420][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:11.422][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:11.424][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:11.425][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:11.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:11.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:11.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:11.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:11.433][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:11.434][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:11.435][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:11.436][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:11.438][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:11.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:11.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:11.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:11.443][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:11.444][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:11.445][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:11.455][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:11.456][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:11.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:11.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:11.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:11.460][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:11.461][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:11.462][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:11.463][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:11.464][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:11.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:11.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:11.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:11.468][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:11.469][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:11.470][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:11.471][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:11.472][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:11.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:11.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:11.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:11.476][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:11.477][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:11.477][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:11.478][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:11.480][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:11.481][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:11.481][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:11.482][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:11.483][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:11.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:11.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:11.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:11.487][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:11.488][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:11.489][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:11.490][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:11.491][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:11.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:11.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:11.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:11.495][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:11.496][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:11.497][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:11.498][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:11.499][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:11.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:11.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:11.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:11.503][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:11.504][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:11.504][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:11.505][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:11.506][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:11.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:11.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:11.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:11.510][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:11.511][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:11.512][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:11.513][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:11.514][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:11.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:11.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:11.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:11.518][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:11.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:11.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:11.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:11.521][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:11.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:11.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:11.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:11.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:11.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:11.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:11.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:11.529][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:11.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:11.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:11.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:11.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:11.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:11.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:11.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:11.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:11.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:11.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:11.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:11.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:11.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:11.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:11.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:11.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:11.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:11.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:11.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:11.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:11.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:11.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:11.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:11.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:11.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:11.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:11.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:11.559][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-05-31 01:53:11.561][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:11.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:11.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:11.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:11.565][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:11.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:11.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:11.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:11.569][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:11.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:11.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:11.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:11.573][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:11.574][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:11.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:11.582][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:11.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:11.584][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:11.585][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[2024-05-31 01:53:11.586][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-05-31 01:53:11.587][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-31 01:53:11.589][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-05-31 01:53:11.590][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-31 01:53:11.592][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-31 01:53:11.593][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-31 01:53:11.594][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-31 01:53:11.595][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-31 01:53:11.596][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-31 01:53:11.599][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:11.600][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:11.601][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:11.606][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:11.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:11.608][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:11.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:11.611][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-05-31 01:53:11.614][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:11.615][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:11.617][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-05-31 01:53:12.013][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-05-31 01:53:12.405][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:12.408][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-05-31 01:53:12.414][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-05-31 01:53:12.418][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-05-31 01:53:12.445][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-31 01:53:12.447][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-31 01:53:12.449][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-31 01:53:12.452][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:12.454][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:12.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:12.461][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:12.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:12.463][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:12.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:12.467][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:12.468][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:12.470][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:12.471][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:12.472][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:12.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:12.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:12.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:12.476][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:12.477][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:12.478][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:12.479][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:12.481][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:12.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:12.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:12.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:12.485][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:12.486][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:12.488][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:12.490][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:12.492][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:12.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:12.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:12.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:12.498][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:12.500][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:12.501][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:12.503][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:12.505][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:12.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:12.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:12.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:12.510][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:12.511][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:12.512][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:12.513][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:12.514][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:12.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:12.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:12.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:12.519][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:12.520][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:12.521][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:12.522][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:12.523][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:12.524][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:12.525][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:12.526][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:12.528][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:12.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:12.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:12.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:12.532][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:12.533][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:12.534][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:12.535][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:12.536][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:12.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:12.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:12.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:12.540][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:12.542][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:12.543][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:12.544][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:12.546][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:12.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:12.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:12.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:12.550][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:12.552][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:12.553][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:12.554][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:12.556][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:12.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:12.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:12.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:12.562][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:12.563][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:12.564][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:12.565][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:12.567][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:12.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:12.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:12.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:12.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:12.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:12.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:12.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:12.574][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:12.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:12.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:12.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:12.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:12.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:12.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:12.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:12.582][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:12.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:12.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:12.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:12.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:12.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:12.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:12.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:12.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:12.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:12.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:12.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:12.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:12.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:12.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:12.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:12.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:12.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:12.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:12.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:12.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:12.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:12.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:12.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:12.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:12.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:12.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:12.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:12.609][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-05-31 01:53:12.610][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:12.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:12.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:12.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:12.616][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:12.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:12.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:12.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:12.621][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:12.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:12.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:12.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:12.627][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:12.628][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:12.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:12.637][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:12.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:12.638][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:12.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:12.640][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-05-31 01:53:12.641][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-31 01:53:12.648][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-05-31 01:53:12.649][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-31 01:53:12.650][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-31 01:53:12.651][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-31 01:53:12.652][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-31 01:53:12.653][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-31 01:53:12.654][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-31 01:53:12.656][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:12.657][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:12.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:12.662][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:12.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:12.664][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:12.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:12.666][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-05-31 01:53:12.669][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:12.670][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:12.671][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-05-31 01:53:13.062][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-05-31 01:53:13.452][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:13.457][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-05-31 01:53:13.464][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-05-31 01:53:13.470][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-05-31 01:53:13.473][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-31 01:53:13.476][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-31 01:53:13.478][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-31 01:53:13.481][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:13.483][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:13.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:13.494][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:13.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:13.497][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:13.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:13.503][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:13.504][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:13.506][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:13.507][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:13.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:13.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:13.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:13.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:13.515][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:13.516][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:13.517][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:13.519][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:13.520][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:13.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:13.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:13.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:13.525][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:13.526][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:13.527][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:13.528][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:13.530][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:13.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:13.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:13.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:13.534][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:13.535][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:13.536][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:13.537][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:13.538][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:13.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:13.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:13.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:13.542][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:13.543][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:13.544][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:13.545][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:13.546][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:13.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:13.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:13.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:13.550][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:13.551][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:13.552][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:13.552][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:13.554][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:13.555][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:13.555][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:13.556][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:13.557][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:13.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:13.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:13.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:13.561][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:13.562][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:13.563][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:13.564][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:13.565][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:13.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:13.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:13.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:13.569][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:13.570][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:13.570][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:13.571][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:13.573][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:13.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:13.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:13.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:13.576][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:13.577][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:13.578][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:13.579][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:13.580][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:13.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:13.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:13.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:13.584][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:13.585][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:13.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:13.586][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:13.588][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:13.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:13.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:13.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:13.591][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:13.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:13.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:13.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:13.595][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:13.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:13.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:13.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:13.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:13.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:13.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:13.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:13.602][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:13.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:13.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:13.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:13.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:13.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:13.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:13.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:13.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:13.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:13.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:13.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:13.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:13.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:13.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:13.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:13.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:13.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:13.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:13.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:13.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:13.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:13.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:13.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:13.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:13.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:13.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:13.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:13.636][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-05-31 01:53:13.637][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:13.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:13.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:13.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:13.640][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:13.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:13.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:13.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:13.644][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:13.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:13.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:13.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:13.648][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:13.648][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:13.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:13.653][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:13.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:13.655][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:13.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:13.657][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-05-31 01:53:13.658][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-31 01:53:13.660][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-05-31 01:53:13.661][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-31 01:53:13.662][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-31 01:53:13.663][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-31 01:53:13.664][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-31 01:53:13.665][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-31 01:53:13.666][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-31 01:53:13.669][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:13.669][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:13.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:13.675][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:13.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:13.676][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:13.677][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[2024-05-31 01:53:13.678][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-05-31 01:53:13.681][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:13.682][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:13.683][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-05-31 01:53:14.076][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-05-31 01:53:14.517][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:14.519][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-05-31 01:53:14.523][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-05-31 01:53:14.525][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-05-31 01:53:14.526][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-31 01:53:14.528][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-31 01:53:14.529][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-31 01:53:14.530][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:14.531][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:14.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:14.536][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:14.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:14.538][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:14.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:14.541][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:14.542][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:14.543][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:14.543][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:14.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:14.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:14.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:14.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:14.551][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:14.553][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:14.554][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:14.555][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:14.557][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:14.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:14.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:14.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:14.561][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:14.562][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:14.563][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:14.564][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:14.566][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:14.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:14.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:14.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:14.570][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:14.571][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:14.572][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:14.573][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:14.574][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:14.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:14.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:14.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:14.578][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:14.580][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:14.580][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:14.581][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:14.583][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:14.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:14.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:14.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:14.587][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:14.588][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:14.589][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:14.590][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:14.591][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:14.592][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:14.593][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:14.594][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:14.595][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:14.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:14.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:14.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:14.601][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:14.602][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:14.603][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:14.604][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:14.605][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:14.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:14.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:14.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:14.609][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:14.610][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:14.611][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:14.612][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:14.613][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:14.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:14.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:14.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:14.619][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:14.621][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:14.622][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:14.624][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:14.626][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:14.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:14.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:14.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:14.631][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:14.632][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:14.633][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:14.634][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:14.689][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:14.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:14.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:14.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:14.693][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:14.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:14.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:14.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:14.697][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:14.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:14.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:14.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:14.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:14.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:14.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:14.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:14.706][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:14.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:14.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:14.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:14.710][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:14.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:14.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:14.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:14.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:14.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:14.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:14.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:14.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:14.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:14.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:14.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:14.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:14.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:14.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:14.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:14.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:14.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:14.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:14.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:14.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:14.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:14.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:14.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:14.733][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-05-31 01:53:14.735][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:14.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:14.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:14.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:14.739][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:14.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:14.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:14.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:14.743][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:14.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:14.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:14.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:14.749][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:14.750][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:14.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:14.755][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:14.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:14.757][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:14.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:14.759][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-05-31 01:53:14.760][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-31 01:53:14.762][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-05-31 01:53:14.763][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-31 01:53:14.764][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-31 01:53:14.765][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-31 01:53:14.766][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-31 01:53:14.767][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-31 01:53:14.768][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-31 01:53:14.771][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:14.772][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:14.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:14.777][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:14.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:14.779][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:14.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:14.781][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-05-31 01:53:14.784][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:14.785][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:14.786][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-05-31 01:53:15.171][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-05-31 01:53:15.566][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:15.569][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-05-31 01:53:15.575][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-05-31 01:53:15.579][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-05-31 01:53:15.582][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-31 01:53:15.584][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-31 01:53:15.586][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-31 01:53:15.589][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:15.591][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:15.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:15.600][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:15.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:15.603][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:15.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:15.609][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:15.610][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:15.612][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:15.613][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:15.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:15.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:15.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:15.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:15.621][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:15.623][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:15.624][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:15.625][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:15.627][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:15.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:15.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:15.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:15.632][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:15.634][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:15.635][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:15.636][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:15.637][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:15.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:15.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:15.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:15.641][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:15.642][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:15.643][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:15.644][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:15.646][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:15.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:15.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:15.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:15.650][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:15.651][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:15.651][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:15.652][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:15.653][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:15.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:15.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:15.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:15.657][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:15.658][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:15.659][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:15.660][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:15.661][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:15.662][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:15.663][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:15.664][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:15.674][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:15.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:15.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:15.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:15.679][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:15.680][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:15.681][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:15.682][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:15.683][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:15.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:15.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:15.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:15.687][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:15.688][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:15.689][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:15.690][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:15.692][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:15.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:15.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:15.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:15.696][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:15.697][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:15.698][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:15.699][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:15.700][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:15.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:15.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:15.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:15.704][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:15.705][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:15.706][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:15.707][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:15.708][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:15.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:15.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:15.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:15.712][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:15.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:15.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:15.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:15.716][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:15.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:15.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:15.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:15.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:15.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:15.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:15.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:15.723][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:15.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:15.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:15.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:15.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:15.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:15.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:15.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:15.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:15.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:15.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:15.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:15.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:15.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:15.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:15.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:15.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:15.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:15.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:15.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:15.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:15.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:15.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:15.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:15.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:15.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:15.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:15.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:15.749][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-05-31 01:53:15.750][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:15.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:15.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:15.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:15.754][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:15.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:15.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:15.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:15.757][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:15.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:15.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:15.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:15.761][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:15.762][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:15.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:15.767][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:15.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:15.769][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:15.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:15.771][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-05-31 01:53:15.772][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-31 01:53:15.773][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-05-31 01:53:15.774][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-31 01:53:15.775][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-31 01:53:15.776][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-31 01:53:15.777][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-31 01:53:15.778][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-31 01:53:15.779][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-31 01:53:15.782][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:15.783][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:15.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:15.788][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:15.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:15.790][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:15.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:15.792][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-05-31 01:53:15.795][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:15.796][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:15.798][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-05-31 01:53:16.189][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-05-31 01:53:16.618][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:16.622][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-05-31 01:53:16.629][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-05-31 01:53:16.635][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-05-31 01:53:16.638][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-31 01:53:16.641][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-31 01:53:16.643][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-31 01:53:16.647][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:16.649][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:16.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:16.660][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:16.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:16.663][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:16.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:16.668][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:16.670][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:16.672][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:16.673][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:16.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:16.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:16.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:16.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:16.681][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:16.682][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:16.684][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:16.685][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:16.687][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:16.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:16.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:16.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:16.700][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:16.702][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:16.703][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:16.704][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:16.705][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:16.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:16.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:16.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:16.709][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:16.710][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:16.711][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:16.712][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:16.713][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:16.714][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:16.715][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:16.716][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:16.717][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:16.718][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:16.719][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:16.720][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:16.721][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:16.722][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:16.723][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:16.723][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:16.725][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:16.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:16.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:16.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:16.728][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:16.729][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:16.730][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:16.731][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:16.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:16.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:16.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:16.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:16.736][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:16.737][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:16.738][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:16.739][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:16.740][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:16.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:16.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:16.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:16.744][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:16.745][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:16.746][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:16.747][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:16.748][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:16.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:16.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:16.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:16.752][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:16.753][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:16.753][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:16.754][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:16.756][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:16.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:16.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:16.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:16.759][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:16.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:16.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:16.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:16.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:16.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:16.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:16.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:16.766][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:16.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:16.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:16.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:16.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:16.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:16.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:16.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:16.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:16.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:16.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:16.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:16.777][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:16.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:16.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:16.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:16.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:16.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:16.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:16.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:16.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:16.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:16.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:16.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:16.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:16.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:16.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:16.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:16.792][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-05-31 01:53:16.793][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:16.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:16.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:16.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:16.797][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:16.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:16.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:16.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:16.801][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:16.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:16.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:16.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:16.804][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:16.805][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:16.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:16.810][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:16.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:16.812][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:16.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:16.814][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-05-31 01:53:16.815][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-31 01:53:16.816][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-05-31 01:53:16.817][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-31 01:53:16.818][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-31 01:53:16.819][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-31 01:53:16.820][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-31 01:53:16.821][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-31 01:53:16.822][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-31 01:53:16.825][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:16.826][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:16.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:16.831][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:16.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:16.833][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:16.833][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[2024-05-31 01:53:16.835][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-05-31 01:53:16.837][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:16.838][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:16.840][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-05-31 01:53:17.229][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2024-05-31 01:53:17.659][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:17.664][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-05-31 01:53:17.671][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-05-31 01:53:17.676][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-05-31 01:53:17.679][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-31 01:53:17.682][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-31 01:53:17.684][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-31 01:53:17.688][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:17.690][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:17.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:17.712][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:17.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:17.715][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:17.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:17.720][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:17.722][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:17.723][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:17.725][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:17.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:17.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:17.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:17.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:17.731][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:17.733][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:17.734][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:17.735][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:17.736][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:17.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:17.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:17.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:17.741][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:17.742][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:17.743][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:17.744][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:17.745][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:17.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:17.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:17.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:17.749][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:17.751][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:17.751][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:17.752][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:17.754][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:17.755][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:17.755][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:17.756][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:17.758][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:17.758][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:17.759][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:17.760][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:17.761][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:17.762][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:17.763][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:17.764][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:17.765][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:17.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:17.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:17.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:17.769][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:17.770][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:17.771][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:17.772][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:17.773][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:17.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:17.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:17.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:17.776][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:17.777][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:17.778][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:17.779][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:17.780][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:17.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:17.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:17.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:17.784][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:17.785][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:17.786][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:17.787][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:17.788][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:17.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:17.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:17.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:17.791][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:17.792][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:17.793][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:17.794][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:17.795][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:17.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:17.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:17.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:17.799][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:17.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:17.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:17.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:17.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:17.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:17.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:17.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:17.806][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:17.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:17.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:17.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:17.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:17.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:17.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:17.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:17.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:17.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:17.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:17.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:17.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:17.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:17.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:17.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:17.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:17.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:17.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:17.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:17.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:17.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:17.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:17.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:17.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:17.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:17.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:17.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:17.837][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-05-31 01:53:17.838][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:17.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:17.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:17.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:17.842][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:17.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:17.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:17.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:17.847][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:17.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:17.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:17.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:17.851][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:17.852][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:17.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:17.859][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:17.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:17.861][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:17.862][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[2024-05-31 01:53:17.863][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-05-31 01:53:17.864][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-31 01:53:17.866][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-05-31 01:53:17.867][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-31 01:53:17.868][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-31 01:53:17.870][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-31 01:53:17.871][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-31 01:53:17.872][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-31 01:53:17.873][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-31 01:53:17.876][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:17.877][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:17.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:17.882][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:17.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:17.884][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:17.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:17.886][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-05-31 01:53:17.889][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:17.890][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:17.905][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-05-31 01:53:18.296][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2024-05-31 01:53:18.725][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:18.729][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-05-31 01:53:18.735][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-05-31 01:53:18.740][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-05-31 01:53:18.742][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-31 01:53:18.745][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-31 01:53:18.747][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-31 01:53:18.750][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:18.752][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:18.754][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:18.762][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:18.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:18.766][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:18.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:18.772][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:18.773][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:18.775][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:18.777][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:18.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:18.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:18.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:18.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:18.784][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:18.786][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:18.787][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:18.788][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:18.790][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:18.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:18.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:18.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:18.795][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:18.796][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:18.797][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:18.798][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:18.799][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:18.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:18.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:18.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:18.804][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:18.805][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:18.806][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:18.807][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:18.808][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:18.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:18.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:18.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:18.812][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:18.813][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:18.814][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:18.815][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:18.816][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:18.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:18.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:18.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:18.820][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:18.821][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:18.822][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:18.823][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:18.824][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:18.825][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:18.826][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:18.827][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:18.828][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:18.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:18.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:18.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:18.832][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:18.833][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:18.834][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:18.835][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:18.836][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:18.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:18.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:18.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:18.840][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:18.841][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:18.842][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:18.843][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:18.845][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:18.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:18.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:18.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:18.849][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:18.850][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:18.850][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:18.851][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:18.853][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:18.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:18.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:18.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:18.856][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:18.857][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:18.858][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:18.859][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:18.860][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:18.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:18.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:18.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:18.864][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:18.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:18.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:18.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:18.868][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:18.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:18.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:18.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:18.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:18.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:18.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:18.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:18.875][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:18.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:18.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:18.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:18.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:18.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:18.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:18.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:18.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:18.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:18.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:18.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:18.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:18.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:18.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:18.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:18.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:18.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:18.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:18.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:18.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:18.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:18.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:18.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:18.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:18.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:18.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:18.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:18.900][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-05-31 01:53:18.901][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:18.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:18.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:18.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:18.905][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:18.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:18.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:18.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:18.908][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:18.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:18.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:18.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:18.912][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:18.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:18.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:18.926][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:18.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:18.928][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:18.929][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[2024-05-31 01:53:18.930][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-05-31 01:53:18.931][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-31 01:53:18.932][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-05-31 01:53:18.933][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-31 01:53:18.934][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-31 01:53:18.935][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-31 01:53:18.936][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-31 01:53:18.937][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-31 01:53:18.938][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-31 01:53:18.941][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:18.942][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:18.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:18.947][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:18.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:18.948][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:18.949][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[2024-05-31 01:53:18.950][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-05-31 01:53:18.953][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:18.954][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:18.955][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-05-31 01:53:19.399][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-05-31 01:53:19.784][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:19.786][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-05-31 01:53:19.789][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-05-31 01:53:19.791][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-05-31 01:53:19.793][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-31 01:53:19.794][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-31 01:53:19.795][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-31 01:53:19.796][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:19.797][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:19.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:19.802][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:19.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:19.804][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:19.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:19.807][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:19.808][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:19.808][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:19.809][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:19.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:19.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:19.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:19.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:19.814][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:19.815][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:19.816][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:19.817][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:19.818][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:19.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:19.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:19.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:19.822][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:19.822][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:19.823][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:19.824][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:19.825][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:19.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:19.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:19.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:19.829][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:19.830][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:19.831][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:19.832][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:19.833][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:19.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:19.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:19.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:19.837][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:19.837][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:19.838][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:19.839][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:19.840][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:19.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:19.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:19.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:19.844][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:19.845][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:19.846][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:19.847][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:19.848][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:19.849][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:19.850][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:19.851][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:19.852][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:19.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:19.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:19.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:19.856][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:19.857][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:19.857][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:19.858][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:19.859][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:19.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:19.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:19.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:19.863][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:19.864][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:19.865][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:19.866][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:19.867][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:19.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:19.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:19.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:19.871][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:19.872][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:19.873][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:19.874][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:19.875][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:19.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:19.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:19.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:19.879][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:19.880][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:19.880][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:19.881][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:19.882][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:19.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:19.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:19.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:19.886][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:19.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:19.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:19.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:19.890][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:19.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:19.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:19.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:19.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:19.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:19.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:19.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:19.897][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:19.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:19.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:19.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:19.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:19.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:19.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:19.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:19.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:19.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:19.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:19.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:19.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:19.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:19.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:19.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:19.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:19.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:19.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:19.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:19.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:19.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:19.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:19.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:19.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:19.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:19.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:19.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:19.931][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-05-31 01:53:19.932][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:19.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:19.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:19.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:19.935][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:19.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:19.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:19.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:19.939][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:19.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:19.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:19.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:19.943][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:19.943][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:19.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:19.949][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:19.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:19.950][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:19.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:19.952][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-05-31 01:53:19.953][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-31 01:53:19.955][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-05-31 01:53:19.956][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-31 01:53:19.957][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-31 01:53:19.958][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-31 01:53:19.959][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-31 01:53:19.959][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-31 01:53:19.960][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-31 01:53:19.963][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:19.963][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:19.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:19.968][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:19.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:19.970][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:19.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:19.972][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-05-31 01:53:19.974][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:19.975][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:19.977][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-05-31 01:53:20.363][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-05-31 01:53:20.751][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:20.754][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-05-31 01:53:20.757][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-05-31 01:53:20.759][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-05-31 01:53:20.760][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-31 01:53:20.761][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-31 01:53:20.762][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-31 01:53:20.764][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:20.765][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:20.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:20.770][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:20.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:20.772][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:20.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:20.775][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:20.776][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:20.777][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:20.778][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:20.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:20.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:20.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:20.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:20.783][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:20.784][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:20.784][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:20.785][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:20.786][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:20.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:20.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:20.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:20.790][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:20.791][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:20.792][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:20.793][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:20.794][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:20.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:20.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:20.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:20.798][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:20.799][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:20.800][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:20.801][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:20.802][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:20.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:20.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:20.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:20.806][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:20.806][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:20.807][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:20.808][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:20.809][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:20.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:20.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:20.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:20.813][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:20.814][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:20.815][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:20.816][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:20.817][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:20.818][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:20.819][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:20.820][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:20.821][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:20.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:20.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:20.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:20.825][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:20.826][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:20.826][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:20.827][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:20.829][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:20.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:20.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:20.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:20.832][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:20.833][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:20.834][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:20.835][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:20.836][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:20.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:20.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:20.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:20.840][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:20.841][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:20.842][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:20.843][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:20.852][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:20.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:20.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:20.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:20.856][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:20.857][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:20.858][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:20.859][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:20.860][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:20.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:20.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:20.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:20.864][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:20.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:20.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:20.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:20.868][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:20.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:20.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:20.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:20.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:20.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:20.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:20.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:20.875][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:20.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:20.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:20.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:20.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:20.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:20.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:20.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:20.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:20.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:20.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:20.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:20.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:20.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:20.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:20.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:20.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:20.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:20.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:20.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:20.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:20.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:20.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:20.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:20.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:20.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:20.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:20.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:20.901][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-05-31 01:53:20.902][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:20.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:20.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:20.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:20.906][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:20.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:20.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:20.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:20.909][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:20.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:20.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:20.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:20.913][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:20.914][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:20.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:20.919][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:20.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:20.920][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:20.921][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[2024-05-31 01:53:20.922][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-05-31 01:53:20.923][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-31 01:53:20.925][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-05-31 01:53:20.926][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-31 01:53:20.927][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-31 01:53:20.928][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-31 01:53:20.929][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-31 01:53:20.930][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-31 01:53:20.931][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-31 01:53:20.933][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:20.934][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:20.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:20.939][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:20.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:20.941][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:20.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:20.943][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-05-31 01:53:20.945][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:20.946][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:20.947][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-05-31 01:53:21.338][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-05-31 01:53:21.771][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:21.774][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-05-31 01:53:21.780][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-05-31 01:53:21.785][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-05-31 01:53:21.788][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-31 01:53:21.790][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-31 01:53:21.792][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-31 01:53:21.795][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:21.797][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:21.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:21.807][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:21.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:21.810][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:21.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:21.816][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:21.818][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:21.819][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:21.821][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:21.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:21.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:21.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:21.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:21.828][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:21.830][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:21.831][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:21.832][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:21.834][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:21.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:21.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:21.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:21.839][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:21.840][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:21.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:21.842][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:21.844][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:21.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:21.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:21.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:21.848][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:21.849][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:21.850][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:21.851][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:21.852][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:21.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:21.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:21.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:21.856][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:21.857][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:21.858][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:21.859][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:21.860][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:21.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:21.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:21.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:21.873][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:21.874][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:21.875][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:21.876][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:21.877][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:21.878][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:21.879][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:21.880][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:21.881][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:21.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:21.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:21.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:21.885][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:21.886][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:21.887][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:21.887][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:21.889][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:21.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:21.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:21.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:21.892][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:21.893][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:21.894][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:21.895][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:21.897][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:21.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:21.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:21.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:21.900][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:21.901][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:21.902][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:21.903][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:21.904][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:21.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:21.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:21.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:21.908][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:21.909][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:21.910][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:21.911][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:21.912][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:21.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:21.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:21.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:21.916][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:21.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:21.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:21.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:21.919][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:21.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:21.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:21.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:21.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:21.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:21.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:21.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:21.927][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:21.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:21.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:21.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:21.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:21.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:21.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:21.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:21.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:21.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:21.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:21.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:21.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:21.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:21.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:21.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:21.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:21.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:21.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:21.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:21.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:21.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:21.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:21.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:21.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:21.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:21.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:21.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:21.952][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-05-31 01:53:21.953][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:21.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:21.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:21.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:21.957][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:21.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:21.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:21.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:21.960][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:21.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:21.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:21.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:21.964][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:21.965][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:21.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:21.970][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:21.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:21.971][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:21.972][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[2024-05-31 01:53:21.973][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-05-31 01:53:21.974][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-31 01:53:21.976][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-05-31 01:53:21.977][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-31 01:53:21.978][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-31 01:53:21.979][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-31 01:53:21.980][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-31 01:53:21.981][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-31 01:53:21.982][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-31 01:53:21.985][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:21.986][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:21.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:21.991][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:21.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:21.993][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:21.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:21.995][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-05-31 01:53:21.997][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:21.998][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:22.000][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-05-31 01:53:22.403][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-05-31 01:53:22.830][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:22.835][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-05-31 01:53:22.842][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-05-31 01:53:22.848][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-05-31 01:53:22.851][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-31 01:53:22.854][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-31 01:53:22.856][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-31 01:53:22.860][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:22.862][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:22.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:22.881][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:22.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:22.886][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:22.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:22.894][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:22.895][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:22.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:22.898][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:22.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:22.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:22.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:22.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:22.928][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:22.929][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:22.930][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:22.931][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:22.932][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:22.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:22.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:22.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:22.936][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:22.937][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:22.938][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:22.939][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:22.941][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:22.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:22.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:22.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:22.945][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:22.946][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:22.947][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:22.947][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:22.949][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:22.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:22.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:22.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:22.953][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:22.954][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:22.955][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:22.956][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:22.957][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:22.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:22.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:22.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:22.961][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:22.962][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:22.963][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:22.964][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:22.965][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:22.966][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:22.967][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:22.968][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:22.969][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:22.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:22.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:22.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:22.973][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:22.974][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:22.975][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:22.976][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:22.977][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:22.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:22.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:22.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:22.981][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:22.982][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:22.983][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:22.984][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:22.986][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:22.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:22.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:22.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:22.990][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:22.991][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:22.992][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:22.992][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:22.994][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:22.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:22.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:22.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:22.998][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:22.999][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:23.000][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:23.001][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:23.002][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:23.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:23.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:23.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:23.006][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:23.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:23.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:23.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:23.010][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:23.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:23.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:23.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:23.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:23.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:23.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:23.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:23.018][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:23.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:23.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:23.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:23.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:23.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:23.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:23.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:23.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:23.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:23.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:23.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:23.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:23.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:23.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:23.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:23.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:23.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:23.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:23.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:23.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:23.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:23.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:23.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:23.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:23.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:23.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:23.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:23.046][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-05-31 01:53:23.047][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:23.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:23.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:23.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:23.051][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:23.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:23.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:23.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:23.055][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:23.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:23.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:23.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:23.059][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:23.060][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:23.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:23.065][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:23.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:23.067][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:23.068][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.DEBUG[2024-05-31 01:53:23.069][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-05-31 01:53:23.070][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-31 01:53:23.071][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-05-31 01:53:23.072][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-31 01:53:23.074][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-31 01:53:23.075][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-31 01:53:23.076][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-31 01:53:23.077][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-31 01:53:23.077][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-31 01:53:23.080][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:23.081][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:23.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:23.086][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:23.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:23.088][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:23.088][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[2024-05-31 01:53:23.090][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-05-31 01:53:23.097][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:23.098][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:23.100][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-05-31 01:53:23.485][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-05-31 01:53:23.878][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:23.883][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-05-31 01:53:23.890][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-05-31 01:53:23.895][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-05-31 01:53:23.898][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-31 01:53:23.901][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-31 01:53:23.903][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-31 01:53:23.907][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:23.908][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:23.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:23.919][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:23.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:23.923][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:23.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:23.928][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:23.930][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:23.931][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:23.933][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:23.935][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:23.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:23.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:23.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:23.941][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:23.942][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:23.943][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:23.945][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:23.946][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:23.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:23.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:23.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:23.951][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:23.953][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:23.954][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:23.955][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:23.956][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:23.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:23.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:23.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:23.961][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:23.962][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:23.963][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:23.964][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:23.965][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:23.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:23.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:23.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:23.969][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:23.970][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:23.971][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:23.972][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:23.973][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:23.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:23.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:23.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:23.977][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:23.978][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:23.979][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:23.979][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:23.981][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:23.982][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:23.982][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:23.983][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:23.984][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:23.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:23.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:23.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:23.988][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:23.989][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:23.990][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:23.991][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:23.992][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:23.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:23.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:23.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:23.996][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:23.997][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:23.998][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:23.998][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.000][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:24.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:24.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.003][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:24.004][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:24.005][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.006][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.007][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:24.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:24.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.011][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:24.012][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:24.013][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.014][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.015][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:24.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:24.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.019][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:24.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:24.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.022][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:24.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:24.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:24.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:24.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.029][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:24.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:24.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:24.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:24.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:24.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:24.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:24.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:24.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:24.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:24.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:24.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:24.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:24.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:24.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:24.055][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-05-31 01:53:24.056][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:24.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:24.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.060][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:24.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:24.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.064][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:24.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:24.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:24.077][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:24.078][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:24.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:24.083][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:24.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:24.085][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:24.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:24.086][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-05-31 01:53:24.087][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-31 01:53:24.089][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-05-31 01:53:24.090][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-31 01:53:24.091][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-31 01:53:24.092][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-31 01:53:24.093][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-31 01:53:24.094][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-31 01:53:24.095][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-31 01:53:24.098][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:24.099][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:24.099][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:24.104][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:24.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:24.106][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:24.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:24.108][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2024-05-31 01:53:24.110][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:24.111][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:24.113][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-05-31 01:53:24.502][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-05-31 01:53:24.890][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:24.892][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-05-31 01:53:24.895][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-05-31 01:53:24.898][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-05-31 01:53:24.899][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-31 01:53:24.900][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-31 01:53:24.901][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-31 01:53:24.903][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:24.904][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:24.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:24.909][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:24.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:24.911][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:24.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:24.914][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:24.915][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:24.915][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.916][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:24.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:24.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.921][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:24.922][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:24.923][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.924][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.925][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:24.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:24.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.929][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:24.930][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:24.931][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.932][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.933][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:24.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:24.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.937][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:24.938][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:24.939][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.940][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.941][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:24.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:24.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.945][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:24.946][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:24.946][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.947][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.949][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:24.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:24.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.952][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:24.953][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:24.954][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.955][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.956][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:24.957][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:24.958][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.959][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.960][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:24.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:24.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.964][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:24.965][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:24.965][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.966][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.967][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:24.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:24.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.971][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:24.972][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:24.973][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.974][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.975][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:24.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:24.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.979][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:24.980][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:24.981][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.982][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.983][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:24.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:24.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.987][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:24.988][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:24.989][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.989][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.991][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:24.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:24.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.994][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:24.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:24.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:24.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:24.998][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:24.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:25.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:25.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:25.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:25.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:25.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:25.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:25.005][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:25.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:25.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:25.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:25.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:25.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:25.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:25.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:25.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:25.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:25.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:25.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:25.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:25.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:25.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:25.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:25.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:25.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:25.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:25.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:25.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:25.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:25.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:25.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:25.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:25.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:25.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:25.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:25.040][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-05-31 01:53:25.041][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:25.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:25.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:25.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:25.045][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:25.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:25.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:25.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:25.049][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:25.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:25.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:25.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:25.069][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[2024-05-31 01:53:25.072][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:25.073][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:25.075][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-05-31 01:53:25.600][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-05-31 01:53:26.162][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:26.164][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-05-31 01:53:26.168][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-05-31 01:53:26.171][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:26.172][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:26.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:26.178][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:26.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:26.179][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:26.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:26.182][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.185][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.189][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:26.193][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:26.194][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:26.195][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:26.199][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:26.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:26.201][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:26.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:26.203][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.207][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.211][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.215][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.219][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:26.223][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:26.223][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:26.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:26.229][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:26.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:26.230][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:26.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:26.232][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.236][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.240][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.243][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.247][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:26.251][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:26.252][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:26.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:26.257][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:26.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:26.259][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:26.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:26.261][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.273][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.277][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.281][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.285][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:26.289][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:26.289][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:26.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:26.295][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:26.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:26.296][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:26.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:26.298][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.302][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.306][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:26.310][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:26.311][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:26.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:26.316][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:26.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:26.317][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:26.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:26.319][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.323][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.327][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:26.331][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:26.331][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:26.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:26.337][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:26.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:26.339][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:26.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:26.341][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.345][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.348][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:26.352][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:26.353][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:26.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:26.359][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:26.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:26.360][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:26.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:26.362][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.366][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.370][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:26.374][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:26.375][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:26.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:26.380][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:26.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:26.381][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:26.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:26.383][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.387][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.391][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:26.394][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:26.395][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:26.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:26.400][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:26.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:26.402][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:26.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:26.404][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.408][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.411][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:26.415][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:26.416][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:26.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:26.421][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:26.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:26.422][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:26.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:26.424][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.428][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.437][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:26.441][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:26.442][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:26.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:26.447][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:26.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:26.448][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:26.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:26.450][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.454][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.458][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:26.461][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:26.462][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:26.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:26.467][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:26.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:26.469][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:26.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:26.471][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.475][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.478][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:26.482][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:26.483][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:26.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:26.488][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:26.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:26.489][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:26.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:26.491][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.495][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.499][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:26.503][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:26.504][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:26.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:26.509][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:26.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:26.511][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:26.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:26.512][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.516][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.520][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:26.523][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:26.524][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:26.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:26.529][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:26.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:26.531][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:26.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:26.533][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.537][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.540][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:26.544][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:26.545][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:26.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:26.550][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:26.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:26.552][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:26.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:26.554][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.558][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.561][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:26.565][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:26.566][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:26.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:26.571][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:26.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:26.573][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:26.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:26.575][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.579][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.582][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:26.586][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:26.587][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:26.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:26.592][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:26.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:26.598][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:26.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:26.600][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.604][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.607][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:26.611][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:26.612][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:26.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:26.617][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:26.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:26.619][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:26.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:26.621][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.624][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.628][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:26.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.644][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:26.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:26.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.648][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:26.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:26.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.651][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:26.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:26.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.655][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:26.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:26.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:26.659][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:26.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:26.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:26.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:26.686][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-31 01:53:26.689][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:26.690][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:26.692][private$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[2024-05-31 01:53:27.109][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[2024-05-31 01:53:27.524][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:27.529][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2024-05-31 01:53:27.537][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2024-05-31 01:53:27.544][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[2024-05-31 01:53:27.551][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:27.553][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:27.557][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-05-31 01:53:27.981][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-05-31 01:53:28.410][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:28.412][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2024-05-31 01:53:28.416][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2024-05-31 01:53:28.419][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:28.419][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:28.420][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:28.424][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:28.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:28.426][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:28.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:28.428][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-05-31 01:53:28.429][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-31 01:53:28.430][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-05-31 01:53:28.432][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-31 01:53:28.433][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-31 01:53:28.434][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-31 01:53:28.435][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-31 01:53:28.435][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-31 01:53:28.436][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-31 01:53:28.439][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:28.440][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:28.440][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:28.445][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:28.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:28.456][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:28.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:28.458][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2024-05-31 01:53:28.461][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:28.462][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:28.463][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2024-05-31 01:53:28.848][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2024-05-31 01:53:29.234][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:29.236][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2024-05-31 01:53:29.239][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2024-05-31 01:53:29.241][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2024-05-31 01:53:29.242][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-31 01:53:29.244][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-31 01:53:29.245][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-31 01:53:29.246][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:29.247][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:29.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:29.252][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:29.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:29.253][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:29.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:29.256][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:29.257][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:29.258][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.259][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:29.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:29.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.264][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:29.265][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:29.266][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.267][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.268][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:29.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:29.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.271][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:29.272][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:29.273][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.274][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.275][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:29.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:29.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.279][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:29.280][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:29.281][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.282][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.283][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:29.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:29.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.286][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:29.287][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:29.288][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.289][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.290][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:29.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:29.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.294][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:29.295][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:29.296][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.296][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.298][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:29.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:29.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.301][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:29.302][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:29.303][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.304][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.305][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:29.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:29.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.312][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:29.314][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:29.315][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.316][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.317][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:29.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:29.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.322][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:29.323][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:29.323][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.324][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.326][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:29.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:29.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.330][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:29.331][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:29.332][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.333][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.334][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:29.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:29.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.338][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:29.339][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:29.340][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.341][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.342][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:29.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:29.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.347][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:29.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:29.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.351][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:29.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:29.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:29.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:29.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.359][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:29.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:29.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:29.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:29.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:29.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:29.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:29.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:29.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:29.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:29.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:29.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:29.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:29.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:29.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:29.386][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-05-31 01:53:29.408][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:29.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:29.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.412][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:29.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:29.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.416][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:29.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:29.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:29.420][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:29.421][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:29.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:29.427][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:29.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:29.429][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:29.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:29.431][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:29.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:29.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.435][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:29.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:29.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:29.439][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:29.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:29.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:29.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:29.443][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:29.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:29.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:29.449][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:29.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:29.451][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:29.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:29.453][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-05-31 01:53:29.454][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-31 01:53:29.455][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-05-31 01:53:29.457][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-31 01:53:29.458][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-31 01:53:29.459][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-31 01:53:29.460][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-31 01:53:29.461][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-31 01:53:29.462][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-31 01:53:29.465][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:29.465][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:29.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:29.471][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:29.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:29.473][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:29.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:29.475][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2024-05-31 01:53:29.477][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:29.478][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:29.480][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2024-05-31 01:53:29.868][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2024-05-31 01:53:30.255][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:30.257][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2024-05-31 01:53:30.261][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2024-05-31 01:53:30.263][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2024-05-31 01:53:30.264][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-31 01:53:30.266][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-31 01:53:30.267][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-31 01:53:30.268][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:30.269][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:30.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:30.274][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:30.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:30.276][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:30.277][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.TRACE[2024-05-31 01:53:30.279][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:30.280][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:30.281][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.282][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:30.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:30.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.286][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:30.287][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:30.288][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.289][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.290][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:30.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:30.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.294][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:30.295][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:30.296][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.297][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.298][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:30.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:30.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.301][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:30.302][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:30.303][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.304][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.305][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:30.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:30.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.309][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:30.310][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:30.311][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.312][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.313][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:30.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:30.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.317][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:30.317][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:30.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.319][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.320][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:30.321][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:30.322][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.323][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.324][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:30.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:30.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.328][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.329][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.330][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.330][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.332][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.335][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:30.336][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:30.337][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.338][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.339][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:30.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:30.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.351][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:30.352][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:30.353][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.354][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.355][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:30.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:30.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.358][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:30.359][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:30.360][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.361][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.362][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:30.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:30.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.366][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:30.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:30.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.370][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:30.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:30.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:30.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:30.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.377][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:30.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:30.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:30.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:30.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:30.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:30.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:30.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:30.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:30.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:30.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:30.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:30.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:30.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:30.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:30.402][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-05-31 01:53:30.403][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.407][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.410][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:30.429][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-31 01:53:30.432][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-31 01:53:30.433][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-31 01:53:30.435][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-31 01:53:30.436][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-05-31 01:53:30.438][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:30.439][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:30.440][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:30.444][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:30.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:30.446][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:30.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:30.448][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.451][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.455][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:30.459][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:30.459][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:30.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:30.464][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:30.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:30.466][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:30.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:30.468][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.472][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.475][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.479][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.483][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:30.486][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:30.487][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:30.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:30.492][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:30.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:30.494][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:30.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:30.496][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.499][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.508][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.512][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.515][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:30.519][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:30.520][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:30.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:30.525][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:30.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:30.526][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:30.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:30.528][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.532][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.536][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.543][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:30.547][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:30.548][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:30.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:30.553][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:30.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:30.554][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:30.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:30.556][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.560][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.564][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:30.567][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:30.568][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:30.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:30.573][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:30.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:30.575][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:30.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:30.576][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.580][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.584][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:30.587][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:30.588][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:30.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:30.593][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:30.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:30.595][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:30.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:30.597][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.600][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.604][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:30.608][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:30.608][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:30.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:30.613][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:30.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:30.615][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:30.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:30.617][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.621][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.624][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:30.628][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:30.629][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:30.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:30.634][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:30.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:30.636][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:30.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:30.638][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.641][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.645][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:30.649][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:30.650][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:30.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:30.655][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:30.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:30.656][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:30.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:30.658][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.667][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.670][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:30.674][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:30.675][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:30.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:30.680][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:30.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:30.681][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:30.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:30.683][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.687][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.690][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:30.694][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:30.695][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:30.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:30.700][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:30.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:30.701][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:30.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:30.703][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.707][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.711][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:30.714][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:30.715][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:30.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:30.720][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:30.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:30.721][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:30.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:30.723][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.727][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.731][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:30.734][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:30.735][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:30.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:30.740][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:30.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:30.742][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:30.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:30.744][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.747][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.751][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:30.755][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:30.755][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:30.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:30.760][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:30.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:30.762][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:30.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:30.764][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.768][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.771][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:30.775][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:30.776][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:30.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:30.781][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:30.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:30.782][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:30.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:30.784][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.788][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.792][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:30.795][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:30.796][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:30.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:30.801][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:30.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:30.803][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:30.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:30.804][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.808][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:30.815][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:30.823][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:30.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:30.830][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:30.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:30.831][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:30.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:30.833][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.837][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.840][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:30.844][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:30.845][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:30.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:30.850][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:30.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:30.852][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:30.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:30.854][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.857][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.861][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:30.864][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:30.865][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:30.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:30.870][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:30.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:30.872][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:30.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:30.874][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.877][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.881][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:30.900][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-31 01:53:30.903][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-31 01:53:30.904][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-31 01:53:30.905][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-31 01:53:30.906][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-05-31 01:53:30.909][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:30.910][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:30.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:30.914][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:30.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:30.916][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:30.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:30.918][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.922][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.925][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:30.929][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:30.930][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:30.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:30.934][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:30.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:30.936][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:30.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:30.938][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.942][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.945][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.949][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.953][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:30.956][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:30.957][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:30.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:30.962][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:30.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:30.964][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:30.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:30.966][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.969][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.973][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.977][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:30.985][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:30.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:30.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:30.990][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:30.990][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:30.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:30.996][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:30.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:30.997][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:30.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:30.999][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.003][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.007][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.011][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.015][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:31.018][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:31.019][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:31.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:31.024][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:31.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:31.026][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:31.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:31.028][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.032][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.035][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:31.039][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:31.040][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:31.041][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:31.045][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:31.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:31.046][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:31.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:31.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.052][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.056][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:31.059][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:31.060][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:31.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:31.065][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:31.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:31.067][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:31.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:31.068][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.072][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.076][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:31.079][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:31.080][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:31.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:31.085][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:31.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:31.087][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:31.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:31.089][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.092][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.096][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:31.100][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:31.100][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:31.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:31.105][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:31.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:31.107][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:31.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:31.109][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.113][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.116][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:31.120][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:31.121][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:31.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:31.126][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:31.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:31.128][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:31.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:31.129][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.133][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.137][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:31.140][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:31.146][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:31.147][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:31.152][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:31.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:31.154][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:31.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:31.156][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.159][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.163][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:31.167][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:31.168][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:31.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:31.173][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:31.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:31.175][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:31.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:31.177][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.181][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.185][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:31.189][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:31.189][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:31.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:31.194][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:31.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:31.196][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:31.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:31.198][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.202][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.205][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:31.209][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:31.210][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:31.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:31.215][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:31.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:31.217][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:31.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:31.219][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.222][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.226][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:31.230][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:31.231][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:31.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:31.236][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:31.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:31.238][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:31.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:31.240][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.243][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.247][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:31.251][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:31.251][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:31.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:31.256][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:31.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:31.258][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:31.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:31.260][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.264][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.267][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:31.271][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:31.272][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:31.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:31.277][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:31.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:31.279][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:31.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:31.281][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.284][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.288][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:31.292][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:31.292][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:31.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:31.297][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:31.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:31.299][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:31.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:31.301][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.305][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.314][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:31.317][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:31.318][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:31.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:31.323][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:31.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:31.325][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:31.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:31.327][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.331][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.334][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:31.338][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:31.339][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:31.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:31.344][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:31.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:31.346][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:31.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:31.348][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.351][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.355][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:31.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.371][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-31 01:53:31.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-31 01:53:31.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-31 01:53:31.381][biodb::testThat]
biodb.INFO [2024-05-31 01:53:31.382][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-05-31 01:53:31.383][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:53:31.383][biodb::testThat]
biodb.TRACE[2024-05-31 01:53:31.386][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-31 01:53:31.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-31 01:53:31.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.390][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:31.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:31.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.394][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:31.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:31.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.397][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:31.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:31.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:31.401][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:31.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:31.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:31.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:31.408][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:31.409][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:31.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:31.414][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:31.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:31.415][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:31.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:31.419][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-31 01:53:31.422][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:31.423][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:31.425][private$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[2024-05-31 01:53:31.811][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[2024-05-31 01:53:32.196][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:32.199][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-05-31 01:53:32.202][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-05-31 01:53:32.205][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:32.205][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:32.206][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:32.210][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:32.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:32.212][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:32.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:32.214][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:32.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:32.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:32.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:32.218][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:32.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:32.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:32.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:32.221][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:32.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:32.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:32.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:32.226][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-31 01:53:32.229][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:32.229][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:32.231][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-05-31 01:53:32.618][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-05-31 01:53:33.002][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:33.004][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-05-31 01:53:33.019][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-05-31 01:53:33.022][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:33.023][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:33.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:33.029][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:33.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:33.031][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:33.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:33.033][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:33.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:33.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:33.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:33.037][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:33.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:33.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:33.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:33.041][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:33.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:33.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:33.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:33.045][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:33.045][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:33.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:33.051][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:33.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:33.053][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:33.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:33.055][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:33.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:33.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:33.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:33.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:33.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:33.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:33.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:33.063][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:33.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:33.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:33.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:33.067][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-31 01:53:33.068][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:33.069][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:33.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:33.074][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:33.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:33.076][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:33.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:33.078][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:33.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:33.082][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:33.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:33.086][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:33.086][private$selectFields]
biodb.TRACE[2024-05-31 01:53:33.087][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-31 01:53:33.088][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-31 01:53:33.089][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:33.090][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.091][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.092][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:33.093][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:33.094][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.094][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.095][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:33.096][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:33.097][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:33.098][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:33.099][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.100][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.101][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:33.102][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:33.103][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-31 01:53:33.104][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:33.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:33.107][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:33.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:33.111][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:33.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:33.123][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-05-31 01:53:33.124][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:33.125][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:33.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:33.130][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:33.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:33.132][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:33.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:33.134][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:33.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:33.138][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:33.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:33.141][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:33.142][private$selectFields]
biodb.TRACE[2024-05-31 01:53:33.143][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-31 01:53:33.144][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-31 01:53:33.145][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:33.146][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.147][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.148][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:33.148][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:33.149][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.150][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.151][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:33.152][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:33.153][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:33.154][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:33.155][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.156][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.157][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:33.157][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:33.158][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-31 01:53:33.159][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:33.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:33.163][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:33.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:33.167][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:33.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:33.171][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-31 01:53:33.172][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:33.173][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:33.178][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:33.183][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:33.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:33.185][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:33.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:33.187][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:33.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:33.190][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:33.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:33.194][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:33.195][private$selectFields]
biodb.TRACE[2024-05-31 01:53:33.196][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-31 01:53:33.196][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-31 01:53:33.197][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:33.198][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.199][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.200][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:33.201][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:33.202][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.203][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.204][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:33.205][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:33.206][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:33.206][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:33.207][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.208][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.209][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:33.210][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:33.211][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-31 01:53:33.212][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:33.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:33.216][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:33.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:33.219][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:33.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:33.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:33.223][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-05-31 01:53:33.224][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-31 01:53:33.225][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-31 01:53:33.234][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:33.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:33.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:33.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:33.238][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:33.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:33.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:33.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:33.241][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:33.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:33.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:33.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:33.245][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:33.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:33.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:33.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:33.300][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:33.301][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:33.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:33.306][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:33.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:33.307][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:33.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:33.311][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-31 01:53:33.314][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:33.315][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:33.317][private$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[2024-05-31 01:53:33.711][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[2024-05-31 01:53:34.102][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:34.107][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-05-31 01:53:34.111][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-05-31 01:53:34.114][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[2024-05-31 01:53:34.117][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:34.117][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:34.119][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-05-31 01:53:34.513][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-05-31 01:53:34.896][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:34.899][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-05-31 01:53:34.902][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-05-31 01:53:34.905][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:34.906][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:34.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:34.911][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:34.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:34.912][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:34.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:34.914][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:34.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:34.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:34.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:34.918][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:34.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:34.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:34.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:34.922][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:34.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:34.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:34.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:34.926][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:34.927][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:34.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:34.932][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:34.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:34.933][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:34.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:34.935][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:34.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:34.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:34.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:34.939][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:34.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:34.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:34.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:34.943][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:34.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:34.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:34.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:34.946][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:34.947][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:34.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:34.952][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:34.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:34.954][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:34.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:34.956][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:34.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:34.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:34.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:34.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:34.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:34.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:34.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:34.963][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:34.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:34.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:34.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:34.989][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-31 01:53:35.012][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:35.013][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:35.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:35.018][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:35.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:35.020][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:35.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:35.022][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.034][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.038][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.039][private$selectFields]
biodb.TRACE[2024-05-31 01:53:35.040][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-31 01:53:35.041][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-31 01:53:35.042][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.043][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.044][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.045][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.046][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.047][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.048][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.049][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.049][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.050][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.051][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.052][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.053][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.054][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.055][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.056][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-31 01:53:35.057][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.061][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.068][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-05-31 01:53:35.070][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:35.070][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:35.071][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:35.075][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:35.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:35.077][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:35.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:35.091][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.094][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.118][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.119][private$selectFields]
biodb.TRACE[2024-05-31 01:53:35.120][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-31 01:53:35.121][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-31 01:53:35.122][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.123][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.124][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.125][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.126][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.127][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.128][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.129][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.130][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.131][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.141][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.142][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.143][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.144][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.145][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.146][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-31 01:53:35.147][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.151][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.155][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.159][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-31 01:53:35.160][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:35.161][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:35.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:35.166][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:35.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:35.168][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:35.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:35.170][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.174][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.178][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.184][private$selectFields]
biodb.TRACE[2024-05-31 01:53:35.185][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-31 01:53:35.186][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-31 01:53:35.187][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.188][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.189][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.190][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.191][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.192][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.193][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.194][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.195][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.196][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.197][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.198][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.199][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.199][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.200][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.201][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-31 01:53:35.202][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.206][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.210][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.214][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-05-31 01:53:35.215][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-31 01:53:35.216][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-31 01:53:35.224][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-31 01:53:35.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-31 01:53:35.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-31 01:53:35.231][biodb::testThat]
biodb.INFO [2024-05-31 01:53:35.231][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-05-31 01:53:35.232][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:53:35.233][biodb::testThat]
biodb.TRACE[2024-05-31 01:53:35.236][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-31 01:53:35.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-31 01:53:35.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.239][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.243][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.247][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.250][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:35.256][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:35.257][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:35.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:35.262][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:35.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:35.264][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:35.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:35.267][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-31 01:53:35.270][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-31 01:53:35.271][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-05-31 01:53:35.272][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-31 01:53:35.273][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-05-31 01:53:35.275][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:35.276][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:35.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:35.281][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:35.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:35.283][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:35.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:35.285][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.289][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.292][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:35.297][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-31 01:53:35.300][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-31 01:53:35.301][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-05-31 01:53:35.302][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-31 01:53:35.303][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-05-31 01:53:35.306][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:35.307][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:35.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:35.312][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:35.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:35.313][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:35.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:35.315][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.319][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.323][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:35.326][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:35.327][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:35.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:35.332][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:35.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:35.334][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:35.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:35.336][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.339][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.348][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:35.352][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-31 01:53:35.354][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:35.355][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:35.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:35.360][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:35.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:35.362][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:35.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:35.364][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.367][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.371][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.372][private$selectFields]
biodb.TRACE[2024-05-31 01:53:35.373][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-31 01:53:35.374][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-31 01:53:35.375][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.375][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.377][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.377][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.378][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.379][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.380][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.381][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.382][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.383][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.384][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.385][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.386][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.387][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.387][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.388][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-31 01:53:35.389][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.393][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.396][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.400][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-05-31 01:53:35.401][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:35.402][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:35.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:35.407][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:35.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:35.409][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:35.410][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.TRACE[2024-05-31 01:53:35.411][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.414][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.418][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.419][private$selectFields]
biodb.TRACE[2024-05-31 01:53:35.420][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-31 01:53:35.421][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-31 01:53:35.422][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.422][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.423][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.424][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.425][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.426][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.427][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.428][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.429][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.430][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.430][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.431][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.432][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.433][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.434][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.435][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-31 01:53:35.436][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.440][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.443][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.447][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-31 01:53:35.448][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:35.449][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:35.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:35.454][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:35.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:35.455][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:35.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:35.462][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.466][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.470][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.471][private$selectFields]
biodb.TRACE[2024-05-31 01:53:35.472][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-31 01:53:35.473][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-31 01:53:35.474][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.475][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.476][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.477][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.478][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.479][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.480][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.481][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.482][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.483][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.484][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.485][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.486][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.487][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.488][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.489][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-31 01:53:35.490][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.494][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.498][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.503][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-05-31 01:53:35.504][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-31 01:53:35.505][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-31 01:53:35.532][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:35.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:35.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.536][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:35.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:35.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.540][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:35.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:35.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.544][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:35.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:35.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:35.550][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:35.551][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:35.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:35.557][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:35.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:35.558][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:35.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:35.562][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-31 01:53:35.565][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-31 01:53:35.567][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-05-31 01:53:35.568][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-31 01:53:35.569][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-05-31 01:53:35.572][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-31 01:53:35.575][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-31 01:53:35.577][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-05-31 01:53:35.578][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-31 01:53:35.579][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-05-31 01:53:35.582][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:35.582][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:35.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:35.588][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:35.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:35.589][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:35.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:35.591][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:35.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:35.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.595][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:35.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:35.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.599][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:35.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:35.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:35.603][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:35.604][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:35.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:35.609][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:35.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:35.611][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:35.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:35.613][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:35.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:35.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.617][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:35.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:35.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.620][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:35.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:35.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:35.624][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:35.625][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:35.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:35.630][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:35.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:35.632][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:35.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:35.634][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:35.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:35.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.638][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:35.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:35.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.642][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:35.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:35.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:35.646][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-31 01:53:35.647][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:35.648][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:35.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:35.653][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:35.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:35.655][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:35.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:35.657][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.660][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.664][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.665][private$selectFields]
biodb.TRACE[2024-05-31 01:53:35.666][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-31 01:53:35.666][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-31 01:53:35.667][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.668][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.669][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.670][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.671][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.672][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.673][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.674][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.674][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.675][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.676][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.677][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.678][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.679][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.680][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.681][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-31 01:53:35.682][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.685][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.694][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.698][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-05-31 01:53:35.699][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:35.700][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:35.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:35.705][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:35.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:35.706][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:35.707][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[2024-05-31 01:53:35.708][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.712][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.716][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.716][private$selectFields]
biodb.TRACE[2024-05-31 01:53:35.717][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-31 01:53:35.718][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-31 01:53:35.719][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.720][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.721][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.722][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.723][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.724][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.725][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.725][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.726][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.727][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.728][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.729][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.730][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.731][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.732][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.733][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-31 01:53:35.733][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.737][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.741][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.745][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-31 01:53:35.746][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:35.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:35.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:35.751][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:35.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:35.753][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:35.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:35.755][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.758][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.762][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.763][private$selectFields]
biodb.TRACE[2024-05-31 01:53:35.764][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-31 01:53:35.765][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-31 01:53:35.765][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.766][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.767][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.768][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.769][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.770][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.771][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.772][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.773][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.773][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.774][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.775][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.776][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.777][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.778][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.779][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-31 01:53:35.780][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.783][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.791][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-05-31 01:53:35.792][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-31 01:53:35.793][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-31 01:53:35.800][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-31 01:53:35.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-31 01:53:35.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-31 01:53:35.806][biodb::testThat]
biodb.INFO [2024-05-31 01:53:35.807][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-05-31 01:53:35.808][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:53:35.809][biodb::testThat]
biodb.TRACE[2024-05-31 01:53:35.812][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-31 01:53:35.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-31 01:53:35.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.815][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.819][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.823][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.826][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:35.833][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:35.834][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:35.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:35.839][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:35.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:35.841][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:35.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:35.849][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-31 01:53:35.852][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-31 01:53:35.854][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-05-31 01:53:35.855][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-31 01:53:35.856][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-05-31 01:53:35.858][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:35.859][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:35.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:35.864][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:35.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:35.865][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:35.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:35.867][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.871][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.875][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:35.879][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-31 01:53:35.882][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-31 01:53:35.883][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-05-31 01:53:35.884][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-31 01:53:35.886][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-05-31 01:53:35.888][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:35.889][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:35.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:35.894][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:35.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:35.895][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:35.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:35.897][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.901][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.904][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:35.908][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:35.909][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:35.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:35.914][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:35.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:35.915][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:35.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:35.917][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.921][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.924][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:35.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:35.928][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-31 01:53:35.930][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:35.930][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:35.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:35.935][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:35.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:35.937][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:35.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:35.939][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.942][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.946][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.947][private$selectFields]
biodb.TRACE[2024-05-31 01:53:35.948][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-31 01:53:35.948][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-31 01:53:35.949][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.950][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.951][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.952][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.953][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.954][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.955][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.956][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.957][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.957][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.958][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.959][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.960][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.961][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.962][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.963][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-31 01:53:35.964][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.967][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.971][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.975][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-05-31 01:53:35.976][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:35.977][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:35.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:35.982][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:35.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:35.983][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:35.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:35.985][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.989][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:35.992][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.993][private$selectFields]
biodb.TRACE[2024-05-31 01:53:35.994][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-31 01:53:35.995][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-31 01:53:35.996][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:35.997][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.998][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:35.999][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:35.999][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.005][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.007][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.008][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.009][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.009][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:36.010][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:36.011][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.012][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.013][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.014][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.015][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-31 01:53:36.016][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.019][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.027][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-31 01:53:36.028][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:36.029][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:36.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:36.034][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:36.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:36.035][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:36.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:36.037][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.041][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.045][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:36.046][private$selectFields]
biodb.TRACE[2024-05-31 01:53:36.046][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-31 01:53:36.047][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-31 01:53:36.048][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:36.049][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.050][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.051][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.052][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.053][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.054][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.054][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.055][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.056][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:36.057][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:36.058][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.059][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.060][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.061][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.061][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-31 01:53:36.062][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.070][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.074][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-05-31 01:53:36.074][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-31 01:53:36.075][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-31 01:53:36.092][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:36.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:36.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.095][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:36.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:36.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.099][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:36.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:36.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.103][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:36.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:36.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:36.110][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:36.111][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:36.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:36.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:36.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:36.118][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:36.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:36.121][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-31 01:53:36.124][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-31 01:53:36.125][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-05-31 01:53:36.127][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-31 01:53:36.128][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-05-31 01:53:36.131][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-31 01:53:36.134][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-31 01:53:36.135][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-05-31 01:53:36.136][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-31 01:53:36.137][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-05-31 01:53:36.140][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:36.140][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:36.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:36.145][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:36.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:36.147][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:36.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:36.149][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:36.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:36.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.153][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:36.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:36.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.156][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:36.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:36.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:36.165][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:36.166][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:36.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:36.171][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:36.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:36.173][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:36.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:36.175][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:36.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:36.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.179][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:36.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:36.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.182][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:36.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:36.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:36.186][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:36.187][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:36.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:36.192][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:36.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:36.194][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:36.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:36.195][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:36.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:36.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.199][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:36.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:36.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.203][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:36.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:36.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:36.207][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-31 01:53:36.208][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:36.209][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:36.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:36.214][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:36.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:36.216][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:36.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:36.217][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.221][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.225][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:36.226][private$selectFields]
biodb.TRACE[2024-05-31 01:53:36.226][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-31 01:53:36.227][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-31 01:53:36.228][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:36.229][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.230][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.231][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.232][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.233][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.234][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.235][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.235][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.236][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:36.237][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:36.238][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.239][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.240][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.241][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.242][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-31 01:53:36.243][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.247][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.250][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.254][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-05-31 01:53:36.255][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:36.256][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:36.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:36.261][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:36.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:36.263][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:36.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:36.265][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.268][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.272][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:36.273][private$selectFields]
biodb.TRACE[2024-05-31 01:53:36.274][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-31 01:53:36.275][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-31 01:53:36.276][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:36.276][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.277][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.278][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.279][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.280][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.281][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.282][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.283][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.284][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:36.285][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:36.286][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.287][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.287][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.288][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.289][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-31 01:53:36.290][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.294][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.297][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.301][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-31 01:53:36.302][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:36.303][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:36.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:36.308][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:36.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:36.310][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:36.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:36.312][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.320][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.324][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:36.325][private$selectFields]
biodb.TRACE[2024-05-31 01:53:36.326][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-31 01:53:36.327][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-31 01:53:36.328][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:36.329][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.329][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.330][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.331][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.332][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.333][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.334][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.335][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.336][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:36.337][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-31 01:53:36.338][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.339][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.339][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.340][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.341][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-31 01:53:36.342][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.346][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.349][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:36.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:36.353][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-05-31 01:53:36.354][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-31 01:53:36.355][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-31 01:53:36.372][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-31 01:53:36.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-31 01:53:36.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:36.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-31 01:53:36.378][biodb::testThat]
biodb.INFO [2024-05-31 01:53:36.379][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2024-05-31 01:53:36.380][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:53:36.381][biodb::testThat]
biodb.DEBUG[2024-05-31 01:53:36.383][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-05-31 01:53:36.384][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-31 01:53:36.385][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-05-31 01:53:36.386][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-31 01:53:36.387][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-31 01:53:36.388][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-31 01:53:36.389][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-31 01:53:36.390][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-31 01:53:36.391][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-31 01:53:36.394][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:36.394][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:36.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:36.399][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:36.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:36.401][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:36.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:36.403][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-05-31 01:53:36.406][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:36.407][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:36.408][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-05-31 01:53:36.793][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-05-31 01:53:37.181][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:37.183][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-05-31 01:53:37.186][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-05-31 01:53:37.188][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-05-31 01:53:37.189][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-31 01:53:37.190][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-31 01:53:37.191][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-31 01:53:37.193][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:37.194][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:37.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:37.199][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:37.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:37.200][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:37.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:37.203][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:37.204][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:37.205][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:37.206][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:37.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:37.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:37.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:37.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:37.211][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:37.212][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:37.213][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:37.213][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:37.215][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:37.215][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:37.216][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:37.217][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:37.219][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:37.219][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:37.220][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:37.221][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:37.222][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:37.223][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:37.224][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:37.225][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:37.226][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:37.227][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:37.228][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:37.229][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:37.230][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:37.231][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:37.232][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:37.233][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:37.234][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:37.235][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:37.236][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:37.236][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:37.237][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:37.238][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:37.239][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:37.240][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:37.241][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:37.251][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:37.252][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:37.253][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:37.254][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:37.255][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:37.256][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:37.257][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:37.258][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:37.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:37.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:37.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:37.262][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:37.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:37.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:37.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:37.265][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:37.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:37.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:37.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:37.269][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:37.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:37.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:37.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:37.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:37.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:37.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:37.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:37.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:37.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:37.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:37.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:37.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:37.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:37.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:37.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:37.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:37.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:37.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:37.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:37.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:37.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:37.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:37.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:37.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:37.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:37.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:37.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:37.295][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-31 01:53:37.296][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-05-31 01:53:37.303][biodb::testThat]
biodb.INFO [2024-05-31 01:53:37.304][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-05-31 01:53:37.305][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:53:37.306][biodb::testThat]
biodb.DEBUG[2024-05-31 01:53:37.314][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-05-31 01:53:37.315][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-05-31 01:53:37.316][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-05-31 01:53:37.317][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-05-31 01:53:37.319][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2024-05-31 01:53:37.320][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-31 01:53:37.321][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-31 01:53:37.322][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-31 01:53:37.323][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-31 01:53:37.324][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-31 01:53:37.327][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:37.328][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:37.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:37.334][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:37.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:37.335][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:37.336][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[2024-05-31 01:53:37.337][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2024-05-31 01:53:37.340][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:37.341][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:37.342][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-05-31 01:53:37.730][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-05-31 01:53:38.123][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:38.125][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-05-31 01:53:38.128][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-05-31 01:53:38.130][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:38.131][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:38.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:38.135][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:38.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:38.137][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:38.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:38.139][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2024-05-31 01:53:38.142][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:38.142][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:38.144][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2024-05-31 01:53:38.613][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2024-05-31 01:53:39.003][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:39.006][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2024-05-31 01:53:39.009][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2024-05-31 01:53:39.010][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:39.011][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:39.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:39.016][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:39.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:39.018][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:39.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:39.020][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2024-05-31 01:53:39.022][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:39.023][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:39.024][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-05-31 01:53:39.412][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2024-05-31 01:53:39.803][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:39.805][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-05-31 01:53:39.808][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-05-31 01:53:39.811][private$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[2024-05-31 01:53:39.812][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-31 01:53:39.813][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-05-31 01:53:39.814][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-05-31 01:53:39.816][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:39.817][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:39.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:39.835][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:39.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:39.837][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:39.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:39.840][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:39.841][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:39.842][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.843][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:39.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:39.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.848][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:39.849][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:39.850][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.850][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.852][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:39.853][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:39.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.854][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.856][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:39.857][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:39.858][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.858][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.860][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:39.861][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:39.861][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.862][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.863][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:39.864][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:39.865][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.866][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.867][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:39.868][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:39.869][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.870][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.871][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:39.872][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:39.873][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.874][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.875][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:39.876][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:39.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.878][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.879][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:39.880][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:39.881][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.882][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.883][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:39.884][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:39.885][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.885][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.887][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:39.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:39.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.890][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:39.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:39.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:39.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:39.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.898][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:39.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:39.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:39.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:39.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:39.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:39.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:39.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:39.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:39.913][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:39.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:39.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:39.919][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:39.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:39.920][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:39.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:39.923][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:39.924][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:39.925][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.926][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:39.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:39.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.931][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:39.932][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:39.933][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.934][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.935][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:39.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:39.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.939][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:39.940][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:39.940][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.941][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.943][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:39.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:39.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.946][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:39.947][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:39.948][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.949][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.950][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:39.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:39.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.954][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:39.955][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:39.956][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.957][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.958][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:39.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:39.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.961][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:39.962][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:39.963][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.964][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.965][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:39.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:39.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.969][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:39.970][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:39.971][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.972][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.973][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:39.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:39.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.976][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:39.977][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:39.978][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.979][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.980][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:39.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:39.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.989][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:39.990][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:39.991][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.992][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.993][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:39.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:39.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:39.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:39.997][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:39.998][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:39.999][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.000][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.001][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:40.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:40.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.004][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:40.005][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:40.006][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.007][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.008][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:40.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:40.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.012][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:40.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:40.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.016][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:40.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:40.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:40.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:40.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:40.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:40.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:40.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:40.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:40.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:40.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:40.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:40.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:40.038][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:40.039][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:40.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:40.044][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:40.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:40.045][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:40.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-31 01:53:40.049][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:40.050][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:40.050][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.051][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:40.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:40.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.056][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:40.057][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:40.058][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.059][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.060][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:40.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:40.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.064][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:40.065][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:40.065][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.066][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.067][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:40.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:40.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.071][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:40.072][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:40.073][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.074][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.075][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:40.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:40.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.079][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:40.080][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:40.080][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.081][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.082][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:40.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:40.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.086][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:40.087][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:40.088][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.089][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.090][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:40.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:40.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.094][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:40.095][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:40.096][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.096][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.098][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:40.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:40.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.101][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:40.102][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:40.103][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.104][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.105][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:40.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:40.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.109][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:40.110][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:40.111][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.112][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.113][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:40.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:40.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.117][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:40.118][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:40.119][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.119][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.121][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:40.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:40.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.124][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:40.125][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:40.126][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.127][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.128][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:40.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:40.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.132][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:40.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:40.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.135][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:40.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:40.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:40.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:40.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.148][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:40.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:40.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.152][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:40.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:40.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:40.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:40.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:40.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:40.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:40.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:40.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:40.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:40.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:40.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:40.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:40.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:40.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:40.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:40.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:40.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:40.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:40.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:40.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:40.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:40.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:40.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:40.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:40.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:40.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:40.196][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-05-31 01:53:40.197][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-31 01:53:40.198][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-05-31 01:53:40.210][biodb::testThat]
biodb.INFO [2024-05-31 01:53:40.211][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2024-05-31 01:53:40.211][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:53:40.212][biodb::testThat]
biodb.INFO [2024-05-31 01:53:40.235][biodb::testThat]
biodb.INFO [2024-05-31 01:53:40.236][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2024-05-31 01:53:40.236][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:53:40.237][biodb::testThat]
biodb.INFO [2024-05-31 01:53:40.244][biodb::testThat]
biodb.INFO [2024-05-31 01:53:40.245][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2024-05-31 01:53:40.246][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:53:40.247][biodb::testThat]
biodb.DEBUG[2024-05-31 01:53:40.249][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2024-05-31 01:53:40.253][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:40.254][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:40.255][private$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[2024-05-31 01:53:40.715][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[2024-05-31 01:53:41.282][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:41.285][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-05-31 01:53:41.292][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-05-31 01:53:41.310][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:41.312][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:41.314][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:41.315][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:41.317][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:41.318][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:41.320][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:41.321][ef$get] fields variable is a list.
biodb.INFO [2024-05-31 01:53:41.324][biodb::testThat]
biodb.INFO [2024-05-31 01:53:41.325][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2024-05-31 01:53:41.326][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:53:41.328][biodb::testThat]
biodb.ERROR[2024-05-31 01:53:41.363][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-05-31 01:53:41.389][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-05-31 01:53:41.402][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-31 01:53:41.404][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-05-31 01:53:41.405][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-05-31 01:53:41.406][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-31 01:53:41.406][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:41.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:41.408][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:41.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:41.410][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-31 01:53:41.420][biodb::testContext]
biodb.INFO [2024-05-31 01:53:41.421][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-31 01:53:41.422][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-05-31 01:53:41.423][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-31 01:53:41.423][biodb::testContext]
biodb.INFO [2024-05-31 01:53:41.425][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-05-31 01:53:41.427][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-05-31 01:53:41.431][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-31 01:53:41.432][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-31 01:53:41.433][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-31 01:53:41.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:41.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:41.436][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-31 01:53:41.437][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-31 01:53:41.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:41.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:41.441][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-31 01:53:41.442][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-31 01:53:41.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:41.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:41.445][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-31 01:53:41.446][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-31 01:53:41.447][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-31 01:53:41.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:41.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:41.450][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-31 01:53:41.451][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-31 01:53:41.452][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-31 01:53:41.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:41.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:41.455][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-31 01:53:41.456][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-31 01:53:41.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:41.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:41.460][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-31 01:53:41.461][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-31 01:53:41.462][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-31 01:53:41.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:41.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:41.465][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-31 01:53:41.466][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-31 01:53:41.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:41.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:41.469][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-31 01:53:41.470][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-31 01:53:41.471][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-31 01:53:41.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:41.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:41.475][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-31 01:53:41.476][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-31 01:53:41.477][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-31 01:53:41.477][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-31 01:53:41.478][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-31 01:53:41.479][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-31 01:53:41.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:41.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:41.483][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-31 01:53:41.484][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-31 01:53:41.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:41.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:41.487][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-31 01:53:41.488][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-31 01:53:41.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:41.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:41.492][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-31 01:53:41.493][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-31 01:53:41.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:41.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:41.496][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-31 01:53:41.497][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-31 01:53:41.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:41.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:41.501][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-31 01:53:41.502][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-31 01:53:41.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:41.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:41.505][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-31 01:53:41.506][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-31 01:53:41.509][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-31 01:53:41.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:41.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:41.513][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-31 01:53:41.514][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-31 01:53:41.514][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-31 01:53:41.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:41.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:41.518][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-31 01:53:41.520][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:41.521][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-31 01:53:41.522][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:41.703][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:53:41.705][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:41.705][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:53:41.706][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:41.707][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-31 01:53:41.708][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-31 01:53:41.709][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:53:41.710][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:41.711][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-31 01:53:41.712][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:53:41.713][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:41.714][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:41.714][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-31 01:53:41.714][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-31 01:53:41.714][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-31 01:53:41.714][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-31 01:53:41.714][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-31 01:53:41.715][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-31 01:53:41.716][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:53:41.717][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:53:41.718][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:53:41.719][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:53:41.720][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:53:41.720][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:53:41.721][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:41.722][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:53:41.723][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:53:41.724][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:41.725][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:41.726][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-31 01:53:41.728][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:41.728][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-31 01:53:41.729][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:41.730][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:53:41.731][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:41.732][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:53:41.733][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:41.734][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-31 01:53:41.735][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-31 01:53:41.736][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:53:41.737][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:41.738][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-31 01:53:41.739][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:53:41.739][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:41.740][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:41.741][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-31 01:53:41.741][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-31 01:53:41.741][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-31 01:53:41.741][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-31 01:53:41.741][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-31 01:53:41.742][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-31 01:53:41.743][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:53:41.744][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:53:41.745][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:53:41.746][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:53:41.747][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:53:41.748][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:53:41.748][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:41.749][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:53:41.750][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:53:41.751][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:41.752][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:41.753][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-31 01:53:41.754][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:41.755][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-31 01:53:41.756][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:41.757][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:53:41.758][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:41.759][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:53:41.760][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:41.761][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-31 01:53:41.762][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-31 01:53:41.762][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:53:41.763][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:41.764][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-31 01:53:41.765][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:53:41.766][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:41.767][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:41.768][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:41.769][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-31 01:53:41.769][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:53:41.770][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:53:41.771][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:53:41.772][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:53:41.773][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:53:41.774][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:53:41.774][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:41.775][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:53:41.776][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:53:41.777][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:41.778][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:41.779][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-31 01:53:41.780][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:41.781][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-31 01:53:41.782][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:41.783][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:53:41.784][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:41.785][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:53:41.786][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:41.787][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-31 01:53:41.787][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-31 01:53:41.788][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:53:41.789][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:41.790][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-31 01:53:41.791][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:53:41.792][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:41.793][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:41.794][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:41.794][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-31 01:53:41.795][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:53:41.796][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:53:41.797][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:53:41.798][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:53:41.799][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:53:41.800][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:53:41.800][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:41.801][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:53:41.802][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:53:41.803][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:41.804][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:41.805][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-31 01:53:41.806][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:41.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:41.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:41.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:41.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:41.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:41.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:41.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:41.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.815][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[2024-05-31 01:53:41.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:41.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:41.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:41.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:41.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:41.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:41.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:41.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.823][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[2024-05-31 01:53:41.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:41.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:41.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:41.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.827][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[2024-05-31 01:53:41.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:41.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:41.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:41.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:41.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:41.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:41.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:41.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:41.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:41.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:41.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:41.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.839][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[2024-05-31 01:53:41.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:41.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:41.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:41.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.843][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[2024-05-31 01:53:41.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:41.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:41.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:41.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:41.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:41.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:41.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:41.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:41.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:41.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:41.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:41.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:41.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:41.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:41.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:41.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:41.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:41.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:41.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:41.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:41.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:41.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:41.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:41.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.868][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[2024-05-31 01:53:41.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:41.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:41.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:41.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.873][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.DEBUG[2024-05-31 01:53:41.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:41.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:41.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:41.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:41.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:41.878][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-31 01:53:41.880][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-31 01:53:41.881][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-31 01:53:41.882][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-31 01:53:41.884][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-31 01:53:41.885][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-31 01:53:41.887][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-31 01:53:41.888][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-31 01:53:41.890][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-31 01:53:41.891][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-31 01:53:41.892][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-31 01:53:41.894][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-31 01:53:41.895][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-31 01:53:41.897][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-31 01:53:41.898][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-31 01:53:41.900][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-31 01:53:41.901][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-31 01:53:41.903][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-31 01:53:41.904][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-31 01:53:41.905][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-31 01:53:41.907][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-31 01:53:41.908][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-31 01:53:41.910][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-31 01:53:41.911][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-31 01:53:41.913][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-31 01:53:41.914][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-31 01:53:41.916][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-31 01:53:41.917][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-31 01:53:41.918][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-31 01:53:41.920][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-31 01:53:41.921][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-31 01:53:41.923][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-31 01:53:41.924][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-31 01:53:41.926][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-31 01:53:41.927][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-31 01:53:41.929][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-31 01:53:41.930][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-31 01:53:41.931][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-31 01:53:41.933][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-31 01:53:41.934][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-31 01:53:41.936][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-31 01:53:41.937][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-31 01:53:41.939][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-31 01:53:41.940][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-31 01:53:41.941][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-31 01:53:41.943][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-31 01:53:41.944][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-31 01:53:41.946][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-31 01:53:41.947][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-31 01:53:41.949][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-31 01:53:41.950][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-31 01:53:41.952][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-31 01:53:41.953][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-31 01:53:41.954][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-31 01:53:41.956][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-31 01:53:41.957][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-31 01:53:41.959][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-31 01:53:41.960][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-31 01:53:41.962][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-31 01:53:41.963][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-31 01:53:41.965][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-31 01:53:41.966][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-31 01:53:41.967][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-31 01:53:41.969][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-31 01:53:41.970][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-31 01:53:41.972][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-31 01:53:41.973][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-31 01:53:41.975][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-31 01:53:41.976][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-31 01:53:41.977][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-31 01:53:41.979][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-31 01:53:41.980][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-31 01:53:41.982][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-31 01:53:41.983][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-31 01:53:41.985][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-31 01:53:41.986][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-31 01:53:41.987][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-31 01:53:41.989][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-31 01:53:41.990][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-31 01:53:41.997][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-31 01:53:41.998][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-31 01:53:42.000][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-31 01:53:42.001][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-31 01:53:42.002][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-31 01:53:42.004][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-05-31 01:53:42.005][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-31 01:53:42.005][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:42.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:42.007][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:42.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:42.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:42.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:42.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:42.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:42.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:42.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:42.013][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[2024-05-31 01:53:42.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:42.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:42.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:42.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:42.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:42.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:42.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:42.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:42.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:42.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:42.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:42.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:42.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:42.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:42.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:42.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:42.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:42.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:42.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:42.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:42.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:42.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:42.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:42.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:42.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:42.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:42.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:42.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:42.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:42.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:42.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:42.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:42.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:42.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:42.042][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.DEBUG[2024-05-31 01:53:42.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:42.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:42.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:42.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:42.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:42.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:42.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:42.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:42.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:42.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:42.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:42.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:42.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:42.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:42.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:42.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:42.056][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:42.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:42.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:42.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:42.059][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[2024-05-31 01:53:42.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:42.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:42.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:42.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:42.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:42.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:42.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:42.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:42.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:42.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:42.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:42.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:42.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:42.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:42.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:42.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:42.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:42.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:42.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:42.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:42.076][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[2024-05-31 01:53:42.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:42.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:42.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:42.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:42.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:42.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:42.081][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[2024-05-31 01:53:42.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:42.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:42.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:42.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:42.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:42.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:42.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:42.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:42.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:42.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:42.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:42.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:42.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:42.092][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[2024-05-31 01:53:42.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:42.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:42.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:42.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:42.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:42.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:42.098][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[2024-05-31 01:53:42.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:42.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:42.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:42.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:42.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:42.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:42.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:42.105][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-05-31 01:53:42.106][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-05-31 01:53:42.108][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:42.109][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-31 01:53:42.110][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:42.111][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:53:42.112][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:42.113][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:53:42.114][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:42.115][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-05-31 01:53:42.116][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-31 01:53:42.116][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:53:42.117][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:42.118][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-05-31 01:53:42.119][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:53:42.120][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-05-31 01:53:42.120][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-05-31 01:53:42.120][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-05-31 01:53:42.120][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-05-31 01:53:42.120][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-05-31 01:53:42.120][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-05-31 01:53:42.120][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-05-31 01:53:42.120][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-05-31 01:53:42.120][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-05-31 01:53:42.120][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-05-31 01:53:42.120][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-05-31 01:53:42.121][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:42.122][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-31 01:53:42.122][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-31 01:53:42.122][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-31 01:53:42.123][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-31 01:53:42.124][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:53:42.125][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:53:42.126][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:53:42.127][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:53:42.128][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:53:42.129][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:53:42.130][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-31 01:53:42.130][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-05-31 01:53:42.131][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:53:42.131][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:53:42.132][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:42.133][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-05-31 01:53:42.133][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-05-31 01:53:42.134][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-31 01:53:42.136][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-31 01:53:42.138][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-05-31 01:53:42.139][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-31 01:53:42.141][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-31 01:53:42.142][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-31 01:53:42.145][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-05-31 01:53:42.146][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-05-31 01:53:42.147][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-05-31 01:53:42.149][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-05-31 01:53:42.150][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-31 01:53:42.151][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-31 01:53:42.152][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-05-31 01:53:42.153][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-05-31 01:53:42.154][biodb::testThat]
biodb.INFO [2024-05-31 01:53:42.155][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2024-05-31 01:53:42.156][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:53:42.157][biodb::testThat]
biodb.DEBUG[2024-05-31 01:53:42.161][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-05-31 01:53:42.164][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:42.165][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:42.167][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2024-05-31 01:53:42.547][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2024-05-31 01:53:43.127][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:43.131][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2024-05-31 01:53:43.138][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2024-05-31 01:53:43.146][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-31 01:53:43.153][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:43.155][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:43.159][private$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[2024-05-31 01:53:43.582][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[2024-05-31 01:53:43.966][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:43.968][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2024-05-31 01:53:43.972][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2024-05-31 01:53:43.974][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:43.975][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:43.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:43.980][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:43.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:43.982][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:43.983][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[2024-05-31 01:53:43.985][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[2024-05-31 01:53:43.988][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:43.989][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:43.990][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-05-31 01:53:44.380][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-05-31 01:53:44.771][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:44.773][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2024-05-31 01:53:44.777][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2024-05-31 01:53:44.779][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:44.780][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:44.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:44.785][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:44.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:44.787][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:44.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:44.804][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:44.805][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:44.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:44.811][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:44.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:44.812][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:44.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:44.818][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-31 01:53:44.821][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-31 01:53:44.823][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-05-31 01:53:44.824][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-31 01:53:44.825][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-05-31 01:53:44.827][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:44.828][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:44.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:44.833][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:44.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:44.834][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:44.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:44.837][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-31 01:53:44.840][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-31 01:53:44.841][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-05-31 01:53:44.842][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-31 01:53:44.843][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-05-31 01:53:44.858][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:44.859][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:44.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:44.863][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:44.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:44.865][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:44.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:44.867][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:44.868][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:44.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:44.881][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:44.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:44.883][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:44.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:44.889][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-31 01:53:44.893][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-31 01:53:44.894][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-05-31 01:53:44.896][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-31 01:53:44.897][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-05-31 01:53:44.899][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:44.900][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:44.901][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:44.905][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:44.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:44.907][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:44.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:44.910][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-31 01:53:44.914][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-31 01:53:44.915][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-05-31 01:53:44.916][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-31 01:53:44.918][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-05-31 01:53:44.919][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:44.920][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:44.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:44.925][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:44.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:44.927][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:44.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:44.930][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-31 01:53:44.933][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:44.934][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:44.936][private$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[2024-05-31 01:53:45.344][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[2024-05-31 01:53:45.762][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:45.766][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2024-05-31 01:53:45.773][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2024-05-31 01:53:45.776][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:45.778][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:45.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:45.787][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:45.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:45.791][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:45.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-31 01:53:45.804][biodb::testThat]
biodb.INFO [2024-05-31 01:53:45.805][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2024-05-31 01:53:45.807][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:53:45.809][biodb::testThat]
biodb.DEBUG[2024-05-31 01:53:45.813][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[2024-05-31 01:53:45.819][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:45.820][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:45.823][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-05-31 01:53:46.230][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-05-31 01:53:46.620][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:46.624][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-05-31 01:53:46.630][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-05-31 01:53:46.634][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:46.636][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:46.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:46.644][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:46.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:46.647][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:46.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:46.655][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-31 01:53:46.660][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:46.662][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:46.665][private$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[2024-05-31 01:53:47.094][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[2024-05-31 01:53:47.507][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:47.509][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-05-31 01:53:47.513][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-05-31 01:53:47.515][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:47.516][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:47.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:47.521][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:47.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:47.523][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-31 01:53:47.528][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-31 01:53:47.529][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-05-31 01:53:47.531][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-05-31 01:53:47.531][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-31 01:53:47.532][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:47.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:47.534][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:47.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:47.536][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-31 01:53:47.540][biodb::testContext]
biodb.INFO [2024-05-31 01:53:47.541][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-31 01:53:47.542][biodb::testContext] Test context - Test web services
biodb.INFO [2024-05-31 01:53:47.543][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-31 01:53:47.544][biodb::testContext]
biodb.INFO [2024-05-31 01:53:47.546][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-05-31 01:53:47.548][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-05-31 01:53:47.552][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-31 01:53:47.553][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-31 01:53:47.554][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-31 01:53:47.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:47.558][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-31 01:53:47.559][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-31 01:53:47.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:47.562][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-31 01:53:47.563][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-31 01:53:47.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:47.567][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-31 01:53:47.568][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-31 01:53:47.569][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-31 01:53:47.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:47.573][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-31 01:53:47.574][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-31 01:53:47.575][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-31 01:53:47.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:47.578][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-31 01:53:47.579][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-31 01:53:47.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:47.583][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-31 01:53:47.584][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-31 01:53:47.585][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-31 01:53:47.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:47.588][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-31 01:53:47.590][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-31 01:53:47.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:47.593][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-31 01:53:47.594][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-31 01:53:47.595][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-31 01:53:47.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:47.599][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-31 01:53:47.600][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-31 01:53:47.601][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-31 01:53:47.602][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-31 01:53:47.603][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-31 01:53:47.604][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-31 01:53:47.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:47.607][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-31 01:53:47.608][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-31 01:53:47.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:47.612][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-31 01:53:47.613][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-31 01:53:47.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.615][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[2024-05-31 01:53:47.616][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-31 01:53:47.617][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-31 01:53:47.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:47.621][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-31 01:53:47.622][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-31 01:53:47.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:47.625][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-31 01:53:47.626][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-31 01:53:47.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:47.630][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-31 01:53:47.631][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-31 01:53:47.634][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-31 01:53:47.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.636][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[2024-05-31 01:53:47.637][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-31 01:53:47.638][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-31 01:53:47.639][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-31 01:53:47.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:47.643][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-31 01:53:47.645][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:47.646][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-31 01:53:47.647][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:47.648][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:53:47.649][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:47.650][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:53:47.651][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:47.652][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-31 01:53:47.653][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-31 01:53:47.654][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:53:47.655][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:47.656][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-31 01:53:47.657][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:53:47.658][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:47.659][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:47.660][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-31 01:53:47.660][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-31 01:53:47.660][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-31 01:53:47.660][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-31 01:53:47.660][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-31 01:53:47.661][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-31 01:53:47.662][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:53:47.662][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:53:47.663][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:53:47.664][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:53:47.665][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:53:47.666][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:53:47.667][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:47.668][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:53:47.669][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:53:47.670][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:47.671][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:47.672][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-31 01:53:47.674][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:47.675][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-31 01:53:47.676][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:47.677][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:53:47.678][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:47.679][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:53:47.698][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:47.699][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-31 01:53:47.700][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-31 01:53:47.701][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:53:47.702][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:47.703][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-31 01:53:47.703][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:53:47.704][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:47.705][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:47.706][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-31 01:53:47.706][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-31 01:53:47.706][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-31 01:53:47.706][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-31 01:53:47.706][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-31 01:53:47.707][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-31 01:53:47.708][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:53:47.709][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:53:47.710][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:53:47.711][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:53:47.712][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:53:47.712][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:53:47.713][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:47.714][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:53:47.715][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:53:47.716][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:47.717][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:47.718][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-31 01:53:47.719][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:47.720][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-31 01:53:47.721][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:47.722][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:53:47.723][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:47.723][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:53:47.724][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:47.725][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-31 01:53:47.726][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-31 01:53:47.727][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:53:47.728][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:47.729][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-31 01:53:47.730][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:53:47.730][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:47.731][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:47.732][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:47.733][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-31 01:53:47.734][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:53:47.735][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:53:47.736][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:53:47.736][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:53:47.737][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:53:47.738][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:53:47.739][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:47.740][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:53:47.740][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:53:47.741][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:47.742][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:47.743][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-31 01:53:47.745][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:47.746][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-31 01:53:47.746][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:47.747][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:53:47.748][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:47.749][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:53:47.750][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:47.751][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-31 01:53:47.752][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-31 01:53:47.753][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:53:47.753][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:47.754][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-31 01:53:47.755][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:53:47.756][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:47.757][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:47.758][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:47.759][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-31 01:53:47.759][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:53:47.760][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:53:47.761][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:53:47.762][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:53:47.763][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:53:47.764][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:53:47.764][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:47.765][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:53:47.766][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:53:47.767][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:47.768][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:47.769][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-31 01:53:47.770][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:47.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:47.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:47.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.774][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[2024-05-31 01:53:47.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:47.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:47.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.778][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[2024-05-31 01:53:47.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:47.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:47.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.782][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[2024-05-31 01:53:47.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:47.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:47.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.786][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[2024-05-31 01:53:47.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:47.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:47.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:47.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:47.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:47.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:47.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:47.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:47.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:47.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:47.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:47.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:47.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:47.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:47.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:47.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:47.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:47.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:47.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:47.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:47.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:47.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:47.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:47.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.818][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[2024-05-31 01:53:47.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:47.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:47.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:47.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:47.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:47.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:47.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:47.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:47.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.830][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.DEBUG[2024-05-31 01:53:47.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:47.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:47.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:47.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:47.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:47.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.838][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[2024-05-31 01:53:47.839][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-31 01:53:47.840][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-31 01:53:47.841][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-31 01:53:47.842][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-31 01:53:47.844][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-31 01:53:47.845][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-31 01:53:47.846][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-31 01:53:47.848][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-31 01:53:47.849][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-31 01:53:47.850][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-31 01:53:47.851][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-31 01:53:47.853][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-31 01:53:47.854][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-31 01:53:47.855][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-31 01:53:47.856][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-31 01:53:47.858][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-31 01:53:47.859][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-31 01:53:47.860][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-31 01:53:47.861][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-31 01:53:47.863][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-31 01:53:47.864][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-31 01:53:47.865][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-31 01:53:47.866][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-31 01:53:47.868][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-31 01:53:47.869][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-31 01:53:47.870][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-31 01:53:47.871][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-31 01:53:47.873][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-31 01:53:47.874][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-31 01:53:47.875][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-31 01:53:47.877][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-31 01:53:47.878][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-31 01:53:47.879][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-31 01:53:47.880][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-31 01:53:47.882][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-31 01:53:47.883][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-31 01:53:47.884][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-31 01:53:47.885][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-31 01:53:47.887][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-31 01:53:47.888][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-31 01:53:47.889][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-31 01:53:47.890][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-31 01:53:47.892][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-31 01:53:47.893][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-31 01:53:47.894][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-31 01:53:47.895][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-31 01:53:47.897][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-31 01:53:47.898][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-31 01:53:47.899][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-31 01:53:47.900][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-31 01:53:47.902][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-31 01:53:47.903][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-31 01:53:47.904][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-31 01:53:47.905][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-31 01:53:47.907][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-31 01:53:47.908][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-31 01:53:47.909][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-31 01:53:47.910][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-31 01:53:47.912][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-31 01:53:47.913][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-31 01:53:47.914][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-31 01:53:47.915][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-31 01:53:47.917][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-31 01:53:47.918][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-31 01:53:47.919][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-31 01:53:47.920][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-31 01:53:47.922][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-31 01:53:47.923][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-31 01:53:47.924][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-31 01:53:47.925][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-31 01:53:47.927][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-31 01:53:47.928][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-31 01:53:47.929][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-31 01:53:47.931][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-31 01:53:47.932][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-31 01:53:47.933][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-31 01:53:47.934][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-31 01:53:47.936][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-31 01:53:47.937][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-31 01:53:47.938][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-31 01:53:47.939][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-31 01:53:47.941][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-31 01:53:47.942][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-31 01:53:47.943][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-31 01:53:47.945][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-05-31 01:53:47.946][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-31 01:53:47.946][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:47.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:47.948][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.949][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[2024-05-31 01:53:47.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:47.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:47.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:47.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:47.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:47.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:47.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:47.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:47.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:47.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:47.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:47.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:47.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:47.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:47.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:47.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:47.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:47.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:47.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:47.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:47.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:47.979][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:47.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:47.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:47.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:47.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:47.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:47.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:47.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:47.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:47.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:47.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:47.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:47.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:47.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:47.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:47.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:47.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:47.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:47.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:47.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:47.998][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[2024-05-31 01:53:47.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:48.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:48.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:48.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:48.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:48.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:48.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:48.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:48.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:48.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:48.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:48.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:48.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:48.009][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[2024-05-31 01:53:48.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:48.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:48.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:48.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:48.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:48.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:48.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:48.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:48.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:48.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:48.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:48.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:48.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:48.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:48.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:48.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:48.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:48.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:48.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:48.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:48.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:48.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:48.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:48.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:48.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:48.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:48.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:48.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:48.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:48.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:48.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:48.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:48.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:48.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:48.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:48.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:48.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:48.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:48.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:48.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:48.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:48.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:48.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:48.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:48.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:48.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:48.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:48.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:48.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:48.048][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-05-31 01:53:48.050][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-05-31 01:53:48.051][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:48.052][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-31 01:53:48.053][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:48.054][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:53:48.055][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:48.056][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:53:48.057][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:48.057][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-05-31 01:53:48.058][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-31 01:53:48.059][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:53:48.060][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:48.061][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-05-31 01:53:48.062][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:53:48.063][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-05-31 01:53:48.063][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-05-31 01:53:48.063][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-05-31 01:53:48.063][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-05-31 01:53:48.063][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-05-31 01:53:48.063][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-05-31 01:53:48.063][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-05-31 01:53:48.063][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-05-31 01:53:48.063][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-05-31 01:53:48.063][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-05-31 01:53:48.063][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-05-31 01:53:48.064][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:48.065][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-31 01:53:48.065][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-31 01:53:48.065][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-31 01:53:48.066][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-31 01:53:48.066][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:53:48.067][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:53:48.068][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:53:48.069][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:53:48.070][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:53:48.070][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:53:48.071][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-31 01:53:48.071][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-05-31 01:53:48.072][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:53:48.073][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:53:48.074][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:48.075][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-05-31 01:53:48.075][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-05-31 01:53:48.076][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-31 01:53:48.078][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-31 01:53:48.079][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-05-31 01:53:48.080][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-31 01:53:48.082][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-31 01:53:48.083][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-31 01:53:48.086][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-05-31 01:53:48.087][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-05-31 01:53:48.088][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-05-31 01:53:48.090][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-05-31 01:53:48.091][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-31 01:53:48.092][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-31 01:53:48.093][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-05-31 01:53:48.094][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-05-31 01:53:48.095][biodb::testThat]
biodb.INFO [2024-05-31 01:53:48.096][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-05-31 01:53:48.097][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:53:48.098][biodb::testThat]
biodb.DEBUG[2024-05-31 01:53:48.100][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-05-31 01:53:48.104][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-31 01:53:48.105][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-05-31 01:53:48.106][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-31 01:53:48.107][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-05-31 01:53:48.110][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[2024-05-31 01:53:48.113][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:48.114][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:48.116][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-05-31 01:53:48.504][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-05-31 01:53:48.891][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:48.893][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-05-31 01:53:48.896][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-05-31 01:53:48.903][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-31 01:53:48.905][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-05-31 01:53:48.906][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-05-31 01:53:48.906][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-31 01:53:48.907][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:48.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:48.909][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:48.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:48.910][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:48.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-31 01:53:48.914][biodb::testContext]
biodb.INFO [2024-05-31 01:53:48.915][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-31 01:53:48.916][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-05-31 01:53:48.917][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-31 01:53:48.918][biodb::testContext]
biodb.INFO [2024-05-31 01:53:48.920][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-05-31 01:53:48.921][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-05-31 01:53:48.925][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-31 01:53:48.926][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-31 01:53:48.926][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-31 01:53:48.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:48.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:48.929][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[2024-05-31 01:53:48.930][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-31 01:53:48.931][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-31 01:53:48.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:48.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:48.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:48.934][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-31 01:53:48.935][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-31 01:53:48.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:48.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:48.937][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[2024-05-31 01:53:48.938][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-31 01:53:48.939][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-31 01:53:48.940][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-31 01:53:48.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:48.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:48.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:48.943][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-31 01:53:48.944][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-31 01:53:48.945][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-31 01:53:48.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:48.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:48.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:48.948][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-31 01:53:48.949][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-31 01:53:48.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:48.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:48.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:48.953][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-31 01:53:48.954][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-31 01:53:48.955][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-31 01:53:48.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:48.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:48.957][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.DEBUG[2024-05-31 01:53:48.958][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-31 01:53:48.959][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-31 01:53:48.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:48.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:48.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:48.962][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-31 01:53:48.963][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-31 01:53:48.964][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-31 01:53:48.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:48.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:48.966][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[2024-05-31 01:53:48.967][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-31 01:53:48.968][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-31 01:53:48.969][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-31 01:53:48.970][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-31 01:53:48.971][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-31 01:53:48.972][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-31 01:53:48.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:48.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:48.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:48.975][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-31 01:53:48.976][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-31 01:53:48.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:48.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:48.978][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[2024-05-31 01:53:48.979][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-31 01:53:48.980][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-31 01:53:48.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:48.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:48.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:48.983][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-31 01:53:48.984][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-31 01:53:48.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:48.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:48.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:48.988][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-31 01:53:48.988][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-31 01:53:48.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:48.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:48.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:48.992][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-31 01:53:48.993][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-31 01:53:48.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:48.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:48.995][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[2024-05-31 01:53:48.996][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-31 01:53:48.997][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-31 01:53:49.000][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-31 01:53:49.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:49.003][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-31 01:53:49.004][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-31 01:53:49.005][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-31 01:53:49.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:49.008][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-31 01:53:49.010][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:49.011][self$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[2024-05-31 01:53:49.012][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:49.013][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:53:49.014][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:49.015][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:53:49.016][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:49.025][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-31 01:53:49.026][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-31 01:53:49.027][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:53:49.028][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:49.029][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-31 01:53:49.029][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:53:49.030][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:49.031][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:49.032][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-31 01:53:49.032][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-31 01:53:49.032][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-31 01:53:49.032][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-31 01:53:49.032][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-31 01:53:49.033][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-31 01:53:49.034][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:53:49.035][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:53:49.035][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:53:49.036][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:53:49.037][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:53:49.038][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:53:49.039][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:49.040][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:53:49.040][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:53:49.041][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:49.042][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:49.043][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-31 01:53:49.045][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:49.046][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-31 01:53:49.047][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:49.048][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:53:49.048][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:49.049][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:53:49.050][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:49.051][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-31 01:53:49.052][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-31 01:53:49.053][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:53:49.054][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:49.055][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-31 01:53:49.055][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:53:49.056][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:49.057][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:49.058][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-31 01:53:49.058][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-31 01:53:49.058][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-31 01:53:49.058][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-31 01:53:49.058][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-31 01:53:49.059][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-31 01:53:49.060][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:53:49.061][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:53:49.062][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:53:49.062][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:53:49.063][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:53:49.064][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:53:49.065][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:49.066][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:53:49.067][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:53:49.067][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:49.068][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:49.069][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-31 01:53:49.071][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:49.072][self$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[2024-05-31 01:53:49.073][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:49.073][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:53:49.074][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:49.075][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:53:49.076][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:49.077][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-31 01:53:49.078][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-31 01:53:49.079][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:53:49.080][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:49.080][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-31 01:53:49.081][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:53:49.082][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:49.083][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:49.084][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:49.085][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-31 01:53:49.086][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:53:49.086][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:53:49.087][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:53:49.088][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:53:49.089][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:53:49.090][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:53:49.091][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:49.092][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:53:49.092][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:53:49.093][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:49.094][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:49.095][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-31 01:53:49.097][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:49.098][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-31 01:53:49.098][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:49.099][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:53:49.100][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:49.101][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:53:49.102][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:49.103][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-31 01:53:49.104][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-31 01:53:49.105][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:53:49.105][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:49.106][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-31 01:53:49.107][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:53:49.108][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:49.109][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:49.110][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:49.111][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-31 01:53:49.112][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:53:49.112][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:53:49.113][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:53:49.114][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:53:49.115][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:53:49.116][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:53:49.117][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:49.117][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:53:49.118][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:53:49.119][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:49.120][self$setPropertyValue]
biodb.DEBUG[2024-05-31 01:53:49.121][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-31 01:53:49.122][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:49.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:49.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.131][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.DEBUG[2024-05-31 01:53:49.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:49.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.139][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.DEBUG[2024-05-31 01:53:49.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:49.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.147][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[2024-05-31 01:53:49.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:49.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:49.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:49.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:49.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:49.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:49.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:49.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:49.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:49.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:49.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:49.192][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-31 01:53:49.194][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-31 01:53:49.195][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-31 01:53:49.196][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-31 01:53:49.198][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-31 01:53:49.199][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-31 01:53:49.200][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-31 01:53:49.201][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-31 01:53:49.203][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-31 01:53:49.204][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-31 01:53:49.205][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-31 01:53:49.207][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-31 01:53:49.208][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-31 01:53:49.209][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-31 01:53:49.210][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-31 01:53:49.212][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-31 01:53:49.213][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-31 01:53:49.214][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-31 01:53:49.215][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-31 01:53:49.217][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-31 01:53:49.218][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-31 01:53:49.219][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-31 01:53:49.220][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-31 01:53:49.222][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-31 01:53:49.223][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-31 01:53:49.224][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-31 01:53:49.225][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-31 01:53:49.227][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-31 01:53:49.228][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-31 01:53:49.229][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-31 01:53:49.231][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-31 01:53:49.232][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-31 01:53:49.233][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-31 01:53:49.234][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-31 01:53:49.236][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-31 01:53:49.237][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-31 01:53:49.238][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-31 01:53:49.239][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-31 01:53:49.241][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-31 01:53:49.242][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-31 01:53:49.243][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-31 01:53:49.244][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-31 01:53:49.246][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-31 01:53:49.247][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-31 01:53:49.248][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-31 01:53:49.250][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-31 01:53:49.251][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-31 01:53:49.252][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-31 01:53:49.253][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-31 01:53:49.255][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-31 01:53:49.256][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-31 01:53:49.257][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-31 01:53:49.259][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-31 01:53:49.260][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-31 01:53:49.261][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-31 01:53:49.262][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-31 01:53:49.264][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-31 01:53:49.265][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-31 01:53:49.266][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-31 01:53:49.268][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-31 01:53:49.269][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-31 01:53:49.270][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-31 01:53:49.271][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-31 01:53:49.273][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-31 01:53:49.274][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-31 01:53:49.275][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-31 01:53:49.277][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-31 01:53:49.278][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-31 01:53:49.279][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-31 01:53:49.280][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-31 01:53:49.282][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-31 01:53:49.283][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-31 01:53:49.284][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-31 01:53:49.285][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-31 01:53:49.287][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-31 01:53:49.288][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-31 01:53:49.289][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-31 01:53:49.295][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-31 01:53:49.296][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-31 01:53:49.298][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-31 01:53:49.299][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-31 01:53:49.300][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-31 01:53:49.301][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-31 01:53:49.303][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-31 01:53:49.304][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-05-31 01:53:49.305][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-31 01:53:49.306][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.307][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.308][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.DEBUG[2024-05-31 01:53:49.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:49.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:49.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.314][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[2024-05-31 01:53:49.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:49.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:49.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:49.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:49.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:49.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:49.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:49.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:49.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.330][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[2024-05-31 01:53:49.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:49.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:49.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.336][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[2024-05-31 01:53:49.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:49.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:49.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:49.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:49.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:49.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:49.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:49.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:49.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.352][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[2024-05-31 01:53:49.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:49.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:49.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:49.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:49.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:49.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:49.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:49.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:49.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.369][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[2024-05-31 01:53:49.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:49.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:49.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.374][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[2024-05-31 01:53:49.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:49.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:49.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:49.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:49.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:49.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:49.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:49.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:49.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:49.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:49.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:49.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:49.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-31 01:53:49.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:49.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:49.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.401][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.DEBUG[2024-05-31 01:53:49.403][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-05-31 01:53:49.404][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-05-31 01:53:49.406][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:49.407][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-31 01:53:49.408][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:49.409][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-31 01:53:49.410][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:49.410][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-31 01:53:49.411][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:49.412][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-05-31 01:53:49.413][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-31 01:53:49.414][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-31 01:53:49.415][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:49.416][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-05-31 01:53:49.417][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-31 01:53:49.418][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-05-31 01:53:49.418][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-05-31 01:53:49.418][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-05-31 01:53:49.418][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-05-31 01:53:49.418][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-05-31 01:53:49.418][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-05-31 01:53:49.418][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-05-31 01:53:49.418][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-05-31 01:53:49.418][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-05-31 01:53:49.418][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-05-31 01:53:49.418][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-05-31 01:53:49.419][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-31 01:53:49.420][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-31 01:53:49.420][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-31 01:53:49.420][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-31 01:53:49.421][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-31 01:53:49.421][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:53:49.422][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:53:49.423][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-31 01:53:49.424][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-31 01:53:49.425][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-31 01:53:49.426][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-31 01:53:49.426][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-31 01:53:49.426][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-05-31 01:53:49.427][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-31 01:53:49.428][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-31 01:53:49.429][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-31 01:53:49.430][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-05-31 01:53:49.430][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-05-31 01:53:49.431][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-31 01:53:49.433][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-31 01:53:49.434][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-05-31 01:53:49.435][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-31 01:53:49.437][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-31 01:53:49.438][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-31 01:53:49.441][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-05-31 01:53:49.442][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-05-31 01:53:49.443][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-05-31 01:53:49.444][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-05-31 01:53:49.446][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-31 01:53:49.446][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-31 01:53:49.448][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-05-31 01:53:49.449][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-05-31 01:53:49.450][biodb::testThat]
biodb.INFO [2024-05-31 01:53:49.451][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-05-31 01:53:49.452][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-31 01:53:49.453][biodb::testThat]
biodb.DEBUG[2024-05-31 01:53:49.455][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-05-31 01:53:49.459][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-31 01:53:49.460][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-05-31 01:53:49.461][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-31 01:53:49.462][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-05-31 01:53:49.465][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-31 01:53:49.468][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-31 01:53:49.469][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-05-31 01:53:49.470][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-31 01:53:49.471][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-05-31 01:53:49.475][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-05-31 01:53:49.476][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-31 01:53:49.478][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-05-31 01:53:49.479][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-31 01:53:49.480][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-31 01:53:49.481][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-31 01:53:49.482][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-31 01:53:49.483][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-31 01:53:49.483][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-31 01:53:49.486][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:49.487][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:49.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:49.491][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:49.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:49.493][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:49.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-31 01:53:49.495][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-05-31 01:53:49.498][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-31 01:53:49.498][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-31 01:53:49.499][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-05-31 01:53:49.910][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2024-05-31 01:53:51.027][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-31 01:53:51.032][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-05-31 01:53:51.039][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-05-31 01:53:51.044][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-05-31 01:53:51.048][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-31 01:53:51.050][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-31 01:53:51.053][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-31 01:53:51.056][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-31 01:53:51.058][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:51.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:51.067][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:51.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:51.070][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:51.071][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.TRACE[2024-05-31 01:53:51.077][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:51.078][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:51.079][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:51.081][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:51.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:51.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:51.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:51.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:51.088][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:51.089][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:51.090][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:51.091][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:51.093][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-31 01:53:51.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-31 01:53:51.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:51.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:51.097][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:51.098][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:51.099][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:51.100][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:51.102][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-31 01:53:51.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-31 01:53:51.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:51.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:51.106][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-31 01:53:51.107][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-31 01:53:51.107][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:51.108][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:51.110][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-31 01:53:51.111][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-31 01:53:51.112][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:51.112][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:51.114][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:51.115][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:51.116][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:51.116][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:51.118][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:51.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-31 01:53:51.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:51.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:51.121][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:51.122][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:51.123][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:51.124][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:51.125][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-31 01:53:51.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-31 01:53:51.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:51.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:51.137][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:51.138][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:51.139][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:51.140][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:51.141][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:51.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-31 01:53:51.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:51.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:51.145][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:51.145][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:51.146][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:51.147][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:51.149][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-31 01:53:51.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-31 01:53:51.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:51.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:51.152][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:51.153][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:51.154][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:51.155][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:51.156][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-31 01:53:51.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-31 01:53:51.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:51.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:51.160][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:51.161][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:51.162][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:51.162][ef$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:51.164][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-31 01:53:51.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-31 01:53:51.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:51.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:51.167][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:51.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:51.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:51.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:51.171][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:51.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:51.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:51.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:51.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:51.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:51.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:51.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:51.178][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-31 01:53:51.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-31 01:53:51.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:51.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:51.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:51.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:51.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:51.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:51.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:51.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:51.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:51.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:51.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:51.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:51.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:51.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:51.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:51.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:51.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:51.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:51.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:51.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:51.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:51.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-31 01:53:51.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-31 01:53:51.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-31 01:53:51.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-31 01:53:51.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-31 01:53:51.203][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-05-31 01:53:51.206][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-31 01:53:51.207][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-05-31 01:53:51.208][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-05-31 01:53:51.209][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-31 01:53:51.209][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-31 01:53:51.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-31 01:53:51.211][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-31 01:53:51.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-31 01:53:51.213][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-31 01:53:51.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
>
> proc.time()
user system elapsed
22.971 0.724 55.812
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 1.054 | 0.084 | 2.318 | |
| ChebiEntry | 0.156 | 0.002 | 0.158 | |