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This page was generated on 2024-05-04 11:36:19 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 200/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbChebi 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/biodbChebi
git_branch: RELEASE_3_19
git_last_commit: fad38a4
git_last_commit_date: 2024-04-30 11:37:31 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    TIMEOUT  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for biodbChebi on nebbiolo1


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.

raw results


Summary

Package: biodbChebi
Version: 1.10.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings biodbChebi_1.10.0.tar.gz
StartedAt: 2024-05-03 21:09:09 -0400 (Fri, 03 May 2024)
EndedAt: 2024-05-03 21:49:09 -0400 (Fri, 03 May 2024)
EllapsedTime: 2400.5 seconds
RetCode: None
Status:   TIMEOUT  
CheckDir: biodbChebi.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings biodbChebi_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
ChebiConn 0.966  0.093  61.501
* 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 ...

Installation output

biodbChebi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL biodbChebi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘biodbChebi’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbChebi)

Tests output

biodbChebi.Rcheck/tests/testthat.Rout


R version 4.4.0 beta (2024-04-15 r86425) -- "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 [2024-05-03 21:10:55.801][biodb::testContext]
biodb.INFO [2024-05-03 21:10:55.804][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-03 21:10:55.805][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-05-03 21:10:55.807][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-03 21:10:55.808][biodb::testContext]
biodb.INFO [2024-05-03 21:10:55.816][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-03 21:10:55.819][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-05-03 21:10:55.828][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-03 21:10:55.830][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-03 21:10:55.831][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-03 21:10:55.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:55.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:55.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:55.836][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-03 21:10:55.857][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-03 21:10:55.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:55.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:55.860][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[2024-05-03 21:10:55.861][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-03 21:10:55.862][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-03 21:10:55.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:55.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:55.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:55.866][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-03 21:10:55.868][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-03 21:10:55.869][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-03 21:10:55.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:55.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:55.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:55.873][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-03 21:10:55.874][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-03 21:10:55.875][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-03 21:10:55.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:55.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:55.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:55.879][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-03 21:10:55.880][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-03 21:10:55.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:55.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:55.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:55.884][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-03 21:10:55.885][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-03 21:10:55.887][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-03 21:10:55.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:55.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:55.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:55.891][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-03 21:10:55.892][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-03 21:10:55.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:55.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:55.895][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[2024-05-03 21:10:55.896][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-03 21:10:55.897][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-03 21:10:55.898][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-03 21:10:55.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:55.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:55.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:55.902][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-03 21:10:55.903][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-03 21:10:55.904][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-03 21:10:55.905][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-03 21:10:55.906][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-03 21:10:55.908][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-03 21:10:55.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:55.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:55.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:55.912][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-03 21:10:55.913][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-03 21:10:55.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:55.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:55.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:55.917][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-03 21:10:55.918][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-03 21:10:55.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:55.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:55.921][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[2024-05-03 21:10:55.922][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-03 21:10:55.923][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-03 21:10:55.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:55.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:55.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:55.927][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-03 21:10:55.928][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-03 21:10:55.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:55.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:55.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:55.932][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-03 21:10:55.933][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-03 21:10:55.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:55.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:55.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:55.937][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-03 21:10:55.938][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-03 21:10:55.943][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-03 21:10:55.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:55.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:55.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:55.947][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-03 21:10:55.949][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-03 21:10:55.950][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-03 21:10:55.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:55.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:55.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:55.957][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-03 21:10:55.997][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-03 21:10:56.025][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-03 21:10:56.026][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 21:10:56.027][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 21:10:56.028][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 21:10:56.029][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 21:10:56.030][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 21:10:56.031][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 21:10:56.032][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-03 21:10:56.033][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 21:10:56.034][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-03 21:10:56.035][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-03 21:10:56.036][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 21:10:56.037][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:10:56.038][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 21:10:56.039][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-03 21:10:56.039][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-03 21:10:56.039][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-03 21:10:56.039][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-03 21:10:56.039][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-03 21:10:56.040][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 21:10:56.041][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:10:56.042][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:10:56.043][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 21:10:56.044][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:10:56.045][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:10:56.046][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 21:10:56.047][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:10:56.048][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 21:10:56.049][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 21:10:56.050][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 21:10:56.051][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:10:56.053][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-03 21:10:56.054][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-03 21:10:56.055][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-03 21:10:56.056][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 21:10:56.057][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 21:10:56.058][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 21:10:56.059][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 21:10:56.060][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 21:10:56.061][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 21:10:56.062][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-03 21:10:56.063][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 21:10:56.064][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-03 21:10:56.065][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-03 21:10:56.066][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 21:10:56.067][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:10:56.068][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 21:10:56.069][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-03 21:10:56.069][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-03 21:10:56.069][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-03 21:10:56.069][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-03 21:10:56.069][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-03 21:10:56.070][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 21:10:56.071][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:10:56.072][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:10:56.073][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 21:10:56.074][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:10:56.075][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:10:56.076][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 21:10:56.077][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:10:56.078][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 21:10:56.079][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 21:10:56.079][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 21:10:56.080][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:10:56.082][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-03 21:10:56.083][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-03 21:10:56.084][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-03 21:10:56.085][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 21:10:56.086][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 21:10:56.087][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 21:10:56.088][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 21:10:56.089][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 21:10:56.090][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 21:10:56.091][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-03 21:10:56.093][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 21:10:56.094][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-03 21:10:56.095][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-03 21:10:56.096][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 21:10:56.097][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:10:56.098][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 21:10:56.099][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:10:56.100][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 21:10:56.101][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:10:56.102][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:10:56.103][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 21:10:56.104][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:10:56.104][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:10:56.105][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 21:10:56.106][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:10:56.107][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 21:10:56.108][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 21:10:56.109][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 21:10:56.110][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:10:56.111][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-03 21:10:56.113][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-03 21:10:56.114][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-03 21:10:56.115][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 21:10:56.116][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 21:10:56.117][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 21:10:56.118][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 21:10:56.119][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 21:10:56.120][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 21:10:56.121][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-03 21:10:56.122][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 21:10:56.123][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-03 21:10:56.124][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-03 21:10:56.125][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 21:10:56.126][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:10:56.127][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 21:10:56.128][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:10:56.129][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 21:10:56.130][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:10:56.131][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:10:56.132][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 21:10:56.133][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:10:56.133][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:10:56.134][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 21:10:56.135][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:10:56.136][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 21:10:56.137][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 21:10:56.138][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 21:10:56.139][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:10:56.143][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-03 21:10:56.144][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:56.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:56.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:56.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:56.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:56.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:56.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.159][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[2024-05-03 21:10:56.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:56.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.163][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[2024-05-03 21:10:56.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:56.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:56.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:56.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:56.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:56.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:56.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:56.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:56.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:56.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.185][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.DEBUG[2024-05-03 21:10:56.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:56.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:56.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:56.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:56.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:56.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:56.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:56.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:56.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:56.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:56.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:56.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:56.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:56.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.216][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.DEBUG[2024-05-03 21:10:56.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:56.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:56.221][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-03 21:10:56.226][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-03 21:10:56.228][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-03 21:10:56.229][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-03 21:10:56.231][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-03 21:10:56.232][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-03 21:10:56.234][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-03 21:10:56.235][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-03 21:10:56.236][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-03 21:10:56.238][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-03 21:10:56.239][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-03 21:10:56.240][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-03 21:10:56.242][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-03 21:10:56.243][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-03 21:10:56.244][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-03 21:10:56.246][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-03 21:10:56.247][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-03 21:10:56.248][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-03 21:10:56.250][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-03 21:10:56.251][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-03 21:10:56.253][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-03 21:10:56.254][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-03 21:10:56.255][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-03 21:10:56.257][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-03 21:10:56.258][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-03 21:10:56.260][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-03 21:10:56.261][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-03 21:10:56.262][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-03 21:10:56.264][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-03 21:10:56.265][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-03 21:10:56.267][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-03 21:10:56.268][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-03 21:10:56.276][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-03 21:10:56.277][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-03 21:10:56.279][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-03 21:10:56.280][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-03 21:10:56.281][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-03 21:10:56.283][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-03 21:10:56.284][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-03 21:10:56.285][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-03 21:10:56.287][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-03 21:10:56.288][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-03 21:10:56.289][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-03 21:10:56.291][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-03 21:10:56.292][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-03 21:10:56.293][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-03 21:10:56.295][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-03 21:10:56.296][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-03 21:10:56.297][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-03 21:10:56.299][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-03 21:10:56.300][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-03 21:10:56.302][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-03 21:10:56.303][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-03 21:10:56.304][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-03 21:10:56.306][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-03 21:10:56.307][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-03 21:10:56.309][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-03 21:10:56.310][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-03 21:10:56.311][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-03 21:10:56.313][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-03 21:10:56.314][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-03 21:10:56.315][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-03 21:10:56.317][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-03 21:10:56.318][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-03 21:10:56.319][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-03 21:10:56.321][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-03 21:10:56.322][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-03 21:10:56.323][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-03 21:10:56.325][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-03 21:10:56.326][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-03 21:10:56.327][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-03 21:10:56.329][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-03 21:10:56.330][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-03 21:10:56.331][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-03 21:10:56.333][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-03 21:10:56.334][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-03 21:10:56.335][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-03 21:10:56.336][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-03 21:10:56.338][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-03 21:10:56.339][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-03 21:10:56.340][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-03 21:10:56.342][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-03 21:10:56.343][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-03 21:10:56.349][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-03 21:10:56.351][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-03 21:10:56.355][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-03 21:10:56.356][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.358][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.358][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[2024-05-03 21:10:56.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:56.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:10:56.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:10:56.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:56.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:56.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:10:56.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:10:56.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:56.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:56.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:10:56.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:10:56.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:56.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:56.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:10:56.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:10:56.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.391][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[2024-05-03 21:10:56.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:56.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:10:56.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:10:56.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:56.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:56.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:10:56.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:10:56.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.409][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[2024-05-03 21:10:56.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:56.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:10:56.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:10:56.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:56.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:56.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:10:56.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:10:56.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:56.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:56.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:10:56.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:10:56.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:56.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:56.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:10:56.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:10:56.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:56.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:56.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:10:56.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:10:56.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:56.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:56.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:10:56.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:10:56.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:56.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:56.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:10:56.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:10:56.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.468][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[2024-05-03 21:10:56.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:56.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:10:56.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:10:56.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:56.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:56.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:10:56.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:10:56.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:56.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:56.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:10:56.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:10:56.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:56.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:10:56.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:10:56.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:10:56.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:10:56.503][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-05-03 21:10:56.515][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-05-03 21:10:56.519][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-03 21:10:56.521][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-03 21:10:56.522][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 21:10:56.524][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 21:10:56.526][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 21:10:56.527][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 21:10:56.529][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-03 21:10:56.530][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-05-03 21:10:56.532][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-03 21:10:56.533][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 21:10:56.535][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-03 21:10:56.537][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-05-03 21:10:56.538][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 21:10:56.539][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-05-03 21:10:56.539][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-05-03 21:10:56.539][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-05-03 21:10:56.539][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-05-03 21:10:56.539][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-05-03 21:10:56.539][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-05-03 21:10:56.539][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-05-03 21:10:56.539][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-05-03 21:10:56.539][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-05-03 21:10:56.539][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-05-03 21:10:56.539][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-05-03 21:10:56.541][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-03 21:10:56.543][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-03 21:10:56.543][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-03 21:10:56.543][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-03 21:10:56.544][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-03 21:10:56.546][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:10:56.547][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:10:56.549][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 21:10:56.550][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:10:56.551][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:10:56.552][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 21:10:56.553][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 21:10:56.553][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-05-03 21:10:56.554][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 21:10:56.556][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 21:10:56.557][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-03 21:10:56.558][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-05-03 21:10:56.558][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-05-03 21:10:56.566][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-03 21:10:56.568][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-03 21:10:56.570][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-05-03 21:10:56.572][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-03 21:10:56.581][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-03 21:10:56.583][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-03 21:10:56.618][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-05-03 21:10:56.620][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-05-03 21:10:56.627][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-05-03 21:10:56.634][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-05-03 21:10:56.642][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-03 21:10:56.643][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-03 21:10:56.646][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-05-03 21:10:56.648][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-05-03 21:10:56.663][biodb::testThat]
biodb.INFO [2024-05-03 21:10:56.664][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-05-03 21:10:56.666][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 21:10:56.668][biodb::testThat]
biodb.TRACE[2024-05-03 21:10:56.674][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-05-03 21:10:56.676][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 21:10:56.681][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 21:10:56.692][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:10:56.694][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:10:56.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:10:56.715][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:56.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:56.718][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:56.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:10:56.732][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:10:56.733][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:10:56.734][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.735][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:10:56.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:10:56.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.754][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:10:56.755][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:10:56.756][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.757][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.786][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:10:56.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:10:56.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.793][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:10:56.794][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:10:56.795][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.796][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.798][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:10:56.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:10:56.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.802][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:10:56.803][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:10:56.804][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.805][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.807][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:10:56.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:10:56.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.811][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:10:56.812][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:10:56.813][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.813][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.815][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:10:56.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:10:56.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.819][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:10:56.820][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:10:56.821][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.822][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.823][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:10:56.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:10:56.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.827][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:10:56.828][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:10:56.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.830][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.831][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:10:56.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:10:56.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.835][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:10:56.836][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:10:56.837][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.838][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.840][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:10:56.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:10:56.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.844][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:10:56.845][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:10:56.846][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.847][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.848][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:10:56.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:10:56.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.852][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:10:56.853][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:10:56.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.855][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.857][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:10:56.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:10:56.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.861][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:10:56.862][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:10:56.863][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.864][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.865][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:10:56.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:10:56.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.870][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:10:56.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:10:56.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.874][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:10:56.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:10:56.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:10:56.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:10:56.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.883][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:10:56.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:10:56.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:10:56.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:10:56.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:10:56.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:10:56.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:10:56.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:10:56.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:10:56.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:10:56.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:10:56.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:10:56.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:10:56.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:10:56.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:10:56.959][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-05-03 21:10:56.961][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:10:56.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:10:56.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.965][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:10:56.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:10:56.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.991][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:10:56.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:10:56.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.995][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:10:56.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:10:56.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:56.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:56.999][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:10:57.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:10:57.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.003][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:10:57.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:10:57.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.007][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-03 21:10:57.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-03 21:10:57.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.011][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-03 21:10:57.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-03 21:10:57.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.014][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-03 21:10:57.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-03 21:10:57.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.018][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-03 21:10:57.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-03 21:10:57.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:10:57.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:10:57.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.054][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:10:57.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:10:57.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:10:57.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:10:57.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:10:57.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:10:57.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:10:57.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:10:57.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:10:57.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:10:57.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:10:57.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:10:57.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:10:57.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:10:57.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.089][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:10:57.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:10:57.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.095][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:10:57.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:10:57.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.100][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:10:57.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:10:57.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:10:57.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:10:57.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:10:57.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:10:57.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:10:57.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:10:57.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.133][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:10:57.135][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:10:57.136][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.138][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:10:57.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:10:57.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.192][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:10:57.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:10:57.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.198][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:10:57.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:10:57.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.204][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:10:57.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:10:57.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.209][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:10:57.210][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:10:57.211][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.213][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.214][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:10:57.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:10:57.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.229][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:10:57.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:10:57.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.234][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:10:57.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:10:57.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.238][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:10:57.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:10:57.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.241][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:10:57.242][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:10:57.243][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.244][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.245][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:10:57.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:10:57.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.257][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:10:57.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:10:57.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.261][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:10:57.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:10:57.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.265][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:10:57.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:10:57.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.269][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:10:57.270][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:10:57.271][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.272][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.273][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:10:57.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:10:57.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.283][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:10:57.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:10:57.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.287][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:10:57.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:10:57.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.291][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:10:57.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:10:57.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.297][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:10:57.298][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:10:57.299][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.301][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.302][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:10:57.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:10:57.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.320][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:10:57.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:10:57.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.327][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:10:57.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:10:57.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:10:57.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:10:57.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.338][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:10:57.340][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:10:57.341][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.342][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.344][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:10:57.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:10:57.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.357][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:10:57.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:10:57.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.363][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:10:57.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:10:57.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.370][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:10:57.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:10:57.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.376][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:10:57.377][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:10:57.379][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.380][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.382][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:10:57.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:10:57.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.401][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-03 21:10:57.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:10:57.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.407][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-03 21:10:57.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:10:57.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.413][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-03 21:10:57.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:10:57.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.419][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-03 21:10:57.421][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:10:57.422][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.423][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.425][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-03 21:10:57.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:10:57.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.443][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:10:57.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:10:57.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.450][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:10:57.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:10:57.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.457][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:10:57.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:10:57.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.463][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:10:57.464][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:10:57.465][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.466][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.467][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:10:57.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:10:57.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.487][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:10:57.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:10:57.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.492][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:10:57.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:10:57.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.497][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:10:57.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:10:57.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.502][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:10:57.503][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:10:57.504][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.505][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.506][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:10:57.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:10:57.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.521][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:10:57.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:10:57.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.528][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:10:57.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:10:57.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.534][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:10:57.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:10:57.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.539][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:10:57.541][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:10:57.542][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.543][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.545][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:10:57.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:10:57.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.564][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:10:57.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:10:57.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.570][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:10:57.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:10:57.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.576][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:10:57.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:10:57.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.583][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:10:57.584][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:10:57.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.587][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.589][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:10:57.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:10:57.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.603][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:10:57.605][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:10:57.607][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.608][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.616][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:10:57.618][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:10:57.620][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.622][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.629][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:10:57.630][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:10:57.631][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.633][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.640][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:10:57.643][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:10:57.644][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.646][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.650][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:10:57.651][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:10:57.653][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.654][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.660][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:10:57.662][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:10:57.664][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.665][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.673][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:10:57.675][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:10:57.677][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.678][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.686][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:10:57.688][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:10:57.690][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.692][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.698][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-03 21:10:57.700][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:10:57.702][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.704][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.712][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:10:57.714][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:10:57.716][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.717][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.722][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:10:57.724][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:10:57.725][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.726][ef$get] fields variable is a list.
biodb.INFO [2024-05-03 21:10:57.733][biodb::testThat]
biodb.INFO [2024-05-03 21:10:57.734][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-05-03 21:10:57.735][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 21:10:57.736][biodb::testThat]
biodb.DEBUG[2024-05-03 21:10:57.750][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-05-03 21:10:57.758][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 21:10:57.764][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-05-03 21:10:57.766][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 21:10:57.767][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-05-03 21:10:57.769][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 21:10:57.812][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 21:10:57.813][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 21:10:57.815][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:10:57.817][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:10:57.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:10:57.826][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:10:57.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:10:57.830][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:10:57.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:10:57.836][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:10:57.837][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:10:57.839][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.841][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:10:57.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:10:57.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.872][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:10:57.874][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:10:57.875][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.876][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.878][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:10:57.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:10:57.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.885][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:10:57.886][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:10:57.888][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.889][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.891][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:10:57.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:10:57.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.897][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:10:57.899][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:10:57.900][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.902][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.904][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:10:57.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:10:57.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.910][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:10:57.911][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:10:57.912][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.913][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.914][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:10:57.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:10:57.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.918][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:10:57.919][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:10:57.920][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.921][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.922][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:10:57.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:10:57.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.926][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:10:57.927][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:10:57.928][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.929][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.930][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:10:57.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:10:57.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.934][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:10:57.935][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:10:57.936][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.937][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.938][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:10:57.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:10:57.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.942][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:10:57.943][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:10:57.944][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.945][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.947][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:10:57.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:10:57.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.951][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:10:57.952][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:10:57.953][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.954][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.955][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:10:57.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:10:57.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.959][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:10:57.960][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:10:57.961][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.962][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.963][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:10:57.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:10:57.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.968][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:10:57.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:10:57.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.972][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:10:57.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:10:57.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:10:57.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:10:57.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.980][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:10:57.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:10:57.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:10:57.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:10:57.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:10:57.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:10:57.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:10:57.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:10:57.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:57.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:10:57.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:10:57.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:57.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:58.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:10:58.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:10:58.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:58.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:58.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:10:58.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:10:58.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:58.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:10:58.008][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-05-03 21:10:58.009][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-05-03 21:10:58.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-05-03 21:10:58.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:58.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:58.013][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-05-03 21:10:58.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-05-03 21:10:58.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:58.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:58.017][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-05-03 21:10:58.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-05-03 21:10:58.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:58.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-03 21:10:58.028][biodb::testThat]
biodb.INFO [2024-05-03 21:10:58.030][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-05-03 21:10:58.031][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 21:10:58.031][biodb::testThat]
biodb.TRACE[2024-05-03 21:10:58.035][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:10:58.036][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:10:58.037][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:58.038][ef$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:10:58.039][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-05-03 21:10:58.070][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:10:58.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:10:58.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:58.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:58.075][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:10:58.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:10:58.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:58.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:10:58.079][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:10:58.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:10:58.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:10:58.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:10:58.086][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-05-03 21:10:58.090][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-05-03 21:10:58.111][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:10:58.113][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:10:58.114][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2024-05-03 21:10:58.669][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2024-05-03 21:10:59.373][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:10:59.376][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2024-05-03 21:10:59.398][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2024-05-03 21:10:59.449][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-03 21:10:59.472][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:10:59.473][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:10:59.495][private$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[2024-05-03 21:11:00.134][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[2024-05-03 21:11:00.788][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:00.793][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-05-03 21:11:00.800][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-05-03 21:11:00.807][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-05-03 21:11:00.822][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:00.824][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:00.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:00.826][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:00.827][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:00.829][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:00.830][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:00.832][ef$get] fields variable is a list.
biodb.INFO [2024-05-03 21:11:00.840][biodb::testThat]
biodb.INFO [2024-05-03 21:11:00.842][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-05-03 21:11:00.843][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 21:11:00.845][biodb::testThat]
biodb.TRACE[2024-05-03 21:11:00.874][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:00.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:00.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:00.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:00.880][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:00.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:00.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:00.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:00.885][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:00.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:00.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:00.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:00.977][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[2024-05-03 21:11:00.981][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 21:11:01.000][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-03 21:11:01.001][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 21:11:01.003][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-05-03 21:11:01.021][biodb::testThat]
biodb.INFO [2024-05-03 21:11:01.022][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-05-03 21:11:01.023][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 21:11:01.024][biodb::testThat]
biodb.TRACE[2024-05-03 21:11:01.049][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:01.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:01.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:01.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:01.055][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:01.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:01.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:01.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:01.059][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:01.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:01.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:01.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:01.064][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:01.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:01.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:01.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:01.067][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:01.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:01.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:01.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:01.072][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:01.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:01.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:01.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:01.076][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-03 21:11:01.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-03 21:11:01.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:01.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:01.080][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-03 21:11:01.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-03 21:11:01.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:01.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:01.084][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-03 21:11:01.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-03 21:11:01.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:01.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:01.088][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-03 21:11:01.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-03 21:11:01.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:01.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:01.113][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:01.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:01.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:01.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:01.119][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:01.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:01.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:01.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:01.123][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:01.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:01.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:01.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:01.128][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:01.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:01.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:01.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:01.135][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:01.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:01.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:01.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:01.138][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:01.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:01.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:01.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:01.142][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-03 21:11:01.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-03 21:11:01.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:01.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:01.146][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-03 21:11:01.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-03 21:11:01.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:01.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:01.151][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-03 21:11:01.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-03 21:11:01.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:01.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:01.155][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-03 21:11:01.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-03 21:11:01.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:01.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-03 21:11:01.167][biodb::testThat]
biodb.INFO [2024-05-03 21:11:01.169][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-05-03 21:11:01.171][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 21:11:01.180][biodb::testThat]
biodb.INFO [2024-05-03 21:11:01.191][biodb::testThat]
biodb.INFO [2024-05-03 21:11:01.192][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-05-03 21:11:01.193][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 21:11:01.194][biodb::testThat]
biodb.INFO [2024-05-03 21:11:01.202][biodb::testThat]
biodb.INFO [2024-05-03 21:11:01.203][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-05-03 21:11:01.204][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 21:11:01.205][biodb::testThat]
biodb.DEBUG[2024-05-03 21:11:01.209][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-05-03 21:11:01.920][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-05-03 21:11:03.345][biodb::testThat]
biodb.INFO [2024-05-03 21:11:03.347][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-05-03 21:11:03.348][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 21:11:03.350][biodb::testThat]
biodb.DEBUG[2024-05-03 21:11:03.865][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[2024-05-03 21:11:04.387][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:04.390][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:04.391][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:04.392][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:04.393][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:04.395][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:04.396][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:04.397][ef$get] fields variable is a list.
biodb.INFO [2024-05-03 21:11:04.401][biodb::testThat]
biodb.INFO [2024-05-03 21:11:04.402][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-05-03 21:11:04.403][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 21:11:04.404][biodb::testThat]
biodb.TRACE[2024-05-03 21:11:04.417][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:04.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:04.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:04.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:04.422][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:04.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:04.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:04.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:04.426][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:04.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:04.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:04.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:04.518][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[2024-05-03 21:11:04.522][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 21:11:04.524][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-03 21:11:04.525][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 21:11:04.526][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-05-03 21:11:04.615][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[2024-05-03 21:11:04.618][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 21:11:04.619][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-03 21:11:04.620][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 21:11:04.621][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-05-03 21:11:04.633][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-03 21:11:04.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-03 21:11:04.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:04.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:04.641][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:04.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:04.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:04.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:04.645][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:04.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:04.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:04.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:04.648][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:04.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:04.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:04.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:04.652][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:04.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:04.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:04.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:04.656][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:04.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:04.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:04.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:04.666][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[2024-05-03 21:11:04.669][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:04.670][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:04.672][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-05-03 21:11:05.132][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-05-03 21:11:05.648][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:05.650][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-05-03 21:11:05.654][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-05-03 21:11:05.657][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:05.658][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:05.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:05.663][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:05.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:05.665][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:05.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:05.667][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-05-03 21:11:05.723][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 21:11:05.725][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-05-03 21:11:05.727][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 21:11:05.728][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 21:11:05.729][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 21:11:05.730][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 21:11:05.731][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 21:11:05.732][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 21:11:05.734][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:05.735][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:05.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:05.741][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:05.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:05.742][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:05.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:05.744][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-05-03 21:11:05.747][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:05.748][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:05.750][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-05-03 21:11:06.209][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-05-03 21:11:06.664][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:06.667][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-05-03 21:11:06.670][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-05-03 21:11:06.673][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-05-03 21:11:06.674][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 21:11:06.676][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 21:11:06.677][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 21:11:06.678][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:06.679][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:06.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:06.685][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:06.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:06.687][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:06.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:06.691][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:06.692][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:06.693][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:06.694][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:06.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:06.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:06.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:06.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:06.699][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:06.701][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:06.702][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:06.703][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:06.704][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:06.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:06.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:06.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:06.709][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:06.710][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:06.711][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:06.712][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:06.714][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:06.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:06.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:06.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:06.718][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:06.719][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:06.720][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:06.721][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:06.722][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:06.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:06.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:06.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:06.726][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:06.728][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:06.728][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:06.729][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:06.731][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:06.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:06.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:06.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:06.735][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:06.736][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:06.737][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:06.738][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:06.739][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:06.740][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:06.741][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:06.742][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:06.743][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:06.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:06.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:06.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:06.747][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:06.748][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:06.749][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:06.750][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:06.751][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:06.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:06.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:06.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:06.755][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:06.756][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:06.757][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:06.758][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:06.760][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:06.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:06.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:06.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:06.764][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:06.765][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:06.766][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:06.767][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:06.768][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:06.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:06.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:06.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:06.772][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:06.773][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:06.774][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:06.775][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:06.776][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:06.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:06.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:06.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:06.780][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:06.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:06.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:06.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:06.784][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:06.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:06.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:06.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:06.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:06.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:06.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:06.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:06.792][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:06.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:06.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:06.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:06.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:06.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:06.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:06.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:06.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:06.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:06.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:06.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:06.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:06.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:06.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:06.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:06.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:06.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:06.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:06.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:06.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:06.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:06.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:06.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:06.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:06.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:06.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:06.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:06.830][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-05-03 21:11:06.840][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:06.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:06.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:06.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:06.845][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:06.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:06.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:06.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:06.849][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:06.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:06.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:06.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:06.854][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-03 21:11:06.857][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:06.858][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:06.860][private$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[2024-05-03 21:11:07.323][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[2024-05-03 21:11:07.801][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:07.805][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-05-03 21:11:07.810][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-05-03 21:11:07.836][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:07.838][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:07.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:07.846][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:07.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:07.849][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:07.851][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.TRACE[2024-05-03 21:11:07.852][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:07.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:07.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:07.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:07.858][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:07.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:07.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:07.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:07.864][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:07.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:07.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:07.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:07.870][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:07.871][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:07.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:07.879][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:07.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:07.882][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:07.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:07.885][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-05-03 21:11:07.887][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 21:11:07.889][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-05-03 21:11:07.891][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 21:11:07.893][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 21:11:07.895][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 21:11:07.896][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 21:11:07.898][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 21:11:07.900][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 21:11:07.915][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:07.916][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:07.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:07.925][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:07.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:07.928][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:07.929][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[2024-05-03 21:11:07.930][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-05-03 21:11:07.934][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:07.935][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:07.937][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-05-03 21:11:08.434][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-05-03 21:11:08.906][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:08.910][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-05-03 21:11:08.914][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-05-03 21:11:08.918][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-05-03 21:11:08.934][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 21:11:08.935][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 21:11:08.937][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 21:11:08.939][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:08.940][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:08.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:08.947][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:08.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:08.949][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:08.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:08.953][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:08.954][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:08.956][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:08.957][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:08.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:08.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:08.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:08.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:08.963][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:08.965][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:08.967][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:08.968][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:08.970][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:08.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:08.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:08.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:08.977][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:08.979][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:08.981][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:08.983][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:08.985][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:08.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:08.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:08.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:08.992][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:08.994][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:08.995][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:08.997][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:08.998][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:09.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:09.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:09.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:09.003][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:09.004][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:09.006][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:09.007][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:09.009][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:09.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:09.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:09.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:09.016][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:09.018][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:09.019][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:09.020][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:09.022][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:09.024][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:09.025][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:09.027][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:09.029][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:09.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:09.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:09.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:09.034][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:09.035][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:09.036][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:09.037][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:09.039][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:09.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:09.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:09.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:09.045][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:09.046][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:09.048][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:09.050][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:09.052][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:09.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:09.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:09.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:09.059][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:09.060][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:09.061][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:09.062][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:09.063][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:09.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:09.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:09.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:09.070][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:09.072][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:09.073][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:09.074][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:09.076][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:09.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:09.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:09.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:09.080][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:09.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:09.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:09.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:09.087][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:09.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:09.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:09.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:09.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:09.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:09.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:09.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:09.098][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:09.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:09.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:09.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:09.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:09.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:09.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:09.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:09.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:09.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:09.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:09.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:09.112][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:09.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:09.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:09.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:09.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:09.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:09.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:09.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:09.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:09.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:09.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:09.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:09.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:09.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:09.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:09.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:09.133][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-05-03 21:11:09.134][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:09.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:09.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:09.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:09.139][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:09.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:09.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:09.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:09.144][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:09.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:09.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:09.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:09.187][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[2024-05-03 21:11:09.194][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 21:11:09.197][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-03 21:11:09.199][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 21:11:09.202][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-05-03 21:11:09.208][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:09.210][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:09.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:09.219][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:09.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:09.222][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:09.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:09.226][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:09.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:09.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:09.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:09.233][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:09.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:09.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:09.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:09.239][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:09.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:09.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:09.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:09.246][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:09.248][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:09.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:09.257][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:09.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:09.261][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:09.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:09.264][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-05-03 21:11:09.266][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 21:11:09.269][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-05-03 21:11:09.271][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 21:11:09.273][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 21:11:09.275][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 21:11:09.277][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 21:11:09.279][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 21:11:09.281][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 21:11:09.286][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:09.288][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:09.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:09.298][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:09.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:09.302][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:09.304][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[2024-05-03 21:11:09.306][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-05-03 21:11:09.312][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:09.313][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:09.315][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-05-03 21:11:09.809][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-05-03 21:11:10.305][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:10.310][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-05-03 21:11:10.322][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-05-03 21:11:10.328][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-05-03 21:11:10.331][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 21:11:10.334][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 21:11:10.337][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 21:11:10.340][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:10.342][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:10.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:10.354][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:10.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:10.356][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:10.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:10.362][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:10.363][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:10.365][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:10.366][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:10.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:10.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:10.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:10.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:10.374][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:10.376][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:10.377][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:10.378][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:10.380][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:10.381][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:10.382][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:10.383][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:10.385][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:10.386][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:10.387][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:10.389][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:10.390][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:10.391][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:10.392][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:10.393][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:10.395][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:10.396][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:10.397][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:10.398][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:10.399][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:10.401][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:10.403][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:10.404][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:10.406][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:10.408][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:10.409][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:10.411][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:10.413][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:10.414][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:10.416][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:10.418][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:10.420][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:10.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:10.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:10.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:10.427][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:10.428][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:10.429][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:10.430][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:10.431][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:10.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:10.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:10.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:10.436][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:10.438][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:10.439][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:10.441][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:10.443][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:10.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:10.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:10.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:10.451][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:10.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:10.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:10.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:10.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:10.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:10.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:10.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:10.465][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:10.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:10.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:10.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:10.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:10.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:10.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:10.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:10.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:10.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:10.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:10.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:10.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:10.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:10.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:10.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:10.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:10.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:10.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:10.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:10.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:10.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:10.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:10.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:10.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:10.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:10.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:10.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:10.536][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-05-03 21:11:10.538][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:10.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:10.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:10.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:10.545][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:10.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:10.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:10.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:10.550][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:10.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:10.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:10.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:10.554][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:10.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:10.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:10.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:10.559][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:10.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:10.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:10.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:10.564][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:10.565][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:10.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:10.578][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:10.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:10.582][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:10.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:10.586][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-05-03 21:11:10.588][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 21:11:10.591][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-05-03 21:11:10.593][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 21:11:10.595][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 21:11:10.597][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 21:11:10.599][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 21:11:10.601][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 21:11:10.602][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 21:11:10.607][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:10.609][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:10.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:10.618][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:10.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:10.622][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:10.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:10.625][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-05-03 21:11:10.630][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:10.631][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:10.634][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-05-03 21:11:11.193][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-05-03 21:11:11.704][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:11.707][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-05-03 21:11:11.712][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-05-03 21:11:11.716][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-05-03 21:11:11.719][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 21:11:11.721][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 21:11:11.722][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 21:11:11.724][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:11.725][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:11.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:11.733][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:11.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:11.735][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:11.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:11.739][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:11.740][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:11.742][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:11.744][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:11.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:11.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:11.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:11.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:11.750][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:11.751][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:11.752][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:11.753][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:11.754][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:11.755][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:11.756][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:11.757][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:11.759][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:11.760][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:11.761][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:11.763][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:11.765][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:11.766][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:11.767][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:11.769][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:11.771][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:11.773][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:11.774][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:11.776][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:11.778][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:11.779][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:11.781][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:11.782][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:11.784][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:11.786][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:11.787][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:11.789][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:11.791][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:11.792][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:11.794][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:11.795][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:11.798][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:11.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:11.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:11.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:11.805][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:11.807][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:11.808][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:11.810][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:11.812][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:11.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:11.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:11.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:11.819][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:11.821][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:11.823][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:11.824][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:11.826][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:11.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:11.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:11.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:11.833][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:11.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:11.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:11.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:11.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:11.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:11.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:11.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:11.864][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:11.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:11.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:11.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:11.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:11.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:11.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:11.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:11.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:11.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:11.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:11.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:11.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:11.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:11.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:11.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:11.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:11.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:11.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:11.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:11.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:11.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:11.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:11.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:11.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:11.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:11.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:11.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:11.907][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-05-03 21:11:11.908][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:11.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:11.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:11.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:11.914][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:11.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:11.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:11.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:11.918][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:11.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:11.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:11.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:11.925][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:11.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:11.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:11.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:11.929][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:11.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:11.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:11.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:11.933][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:11.934][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:11.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:11.943][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:11.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:11.947][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:11.949][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[2024-05-03 21:11:11.950][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-05-03 21:11:11.951][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 21:11:11.954][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-05-03 21:11:11.957][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 21:11:11.959][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 21:11:11.961][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 21:11:11.962][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 21:11:11.964][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 21:11:11.966][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 21:11:11.971][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:11.972][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:11.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:11.982][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:11.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:11.985][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:11.987][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[2024-05-03 21:11:11.989][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-05-03 21:11:11.994][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:11.996][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:12.002][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-05-03 21:11:12.515][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-05-03 21:11:13.030][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:13.036][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-05-03 21:11:13.043][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-05-03 21:11:13.049][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-05-03 21:11:13.052][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 21:11:13.054][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 21:11:13.057][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 21:11:13.061][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:13.063][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:13.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:13.074][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:13.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:13.077][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:13.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:13.081][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:13.083][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:13.085][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:13.086][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:13.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:13.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:13.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:13.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:13.095][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:13.097][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:13.098][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:13.100][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:13.102][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:13.104][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:13.106][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:13.107][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:13.109][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:13.110][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:13.111][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:13.112][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:13.113][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:13.115][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:13.116][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:13.118][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:13.120][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:13.122][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:13.123][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:13.124][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:13.126][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:13.128][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:13.130][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:13.131][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:13.134][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:13.136][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:13.137][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:13.139][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:13.141][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:13.143][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:13.145][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:13.146][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:13.149][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:13.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:13.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:13.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:13.155][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:13.157][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:13.158][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:13.159][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:13.183][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:13.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:13.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:13.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:13.194][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:13.195][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:13.196][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:13.197][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:13.199][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:13.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:13.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:13.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:13.204][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:13.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:13.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:13.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:13.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:13.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:13.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:13.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:13.214][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:13.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:13.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:13.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:13.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:13.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:13.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:13.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:13.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:13.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:13.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:13.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:13.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:13.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:13.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:13.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:13.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:13.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:13.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:13.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:13.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:13.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:13.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:13.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:13.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:13.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:13.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:13.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:13.254][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-05-03 21:11:13.256][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:13.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:13.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:13.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:13.262][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:13.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:13.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:13.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:13.269][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:13.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:13.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:13.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:13.276][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:13.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:13.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:13.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:13.283][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:13.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:13.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:13.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:13.290][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:13.291][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:13.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:13.299][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:13.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:13.301][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:13.302][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[2024-05-03 21:11:13.304][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-05-03 21:11:13.305][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 21:11:13.308][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-05-03 21:11:13.311][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 21:11:13.313][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 21:11:13.315][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 21:11:13.316][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 21:11:13.318][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 21:11:13.320][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 21:11:13.324][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:13.326][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:13.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:13.332][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:13.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:13.334][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:13.335][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.DEBUG[2024-05-03 21:11:13.336][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-05-03 21:11:13.341][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:13.343][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:13.345][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-05-03 21:11:13.830][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-05-03 21:11:14.317][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:14.320][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-05-03 21:11:14.323][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-05-03 21:11:14.328][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-05-03 21:11:14.331][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 21:11:14.333][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 21:11:14.335][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 21:11:14.337][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:14.339][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:14.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:14.348][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:14.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:14.351][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:14.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:14.356][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:14.357][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:14.358][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.359][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:14.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:14.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:14.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:14.367][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:14.369][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:14.371][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.372][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:14.374][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:14.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:14.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:14.381][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:14.383][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:14.384][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.385][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:14.387][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:14.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:14.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:14.393][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:14.394][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:14.395][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.396][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:14.397][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:14.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:14.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:14.401][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:14.402][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:14.404][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.406][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:14.416][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:14.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:14.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:14.429][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:14.431][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:14.432][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.433][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:14.435][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:14.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:14.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:14.439][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:14.440][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:14.442][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.443][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:14.445][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:14.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:14.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:14.449][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:14.450][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:14.451][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.452][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:14.453][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:14.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:14.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:14.457][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:14.458][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:14.459][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.460][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:14.462][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:14.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:14.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:14.469][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:14.471][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:14.472][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.474][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:14.476][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:14.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:14.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:14.482][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:14.484][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:14.485][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.487][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:14.489][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:14.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:14.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:14.496][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:14.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:14.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:14.502][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:14.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:14.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:14.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:14.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:14.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:14.512][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:14.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:14.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:14.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:14.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:14.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:14.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:14.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:14.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:14.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:14.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:14.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:14.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:14.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:14.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:14.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:14.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:14.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:14.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:14.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:14.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:14.554][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-05-03 21:11:14.555][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:14.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:14.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:14.560][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:14.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:14.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:14.564][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:14.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:14.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:14.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:14.569][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:14.571][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:14.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:14.576][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:14.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:14.578][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:14.579][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[2024-05-03 21:11:14.580][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-05-03 21:11:14.581][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 21:11:14.583][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-05-03 21:11:14.584][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 21:11:14.585][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 21:11:14.586][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 21:11:14.588][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 21:11:14.589][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 21:11:14.591][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 21:11:14.595][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:14.596][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:14.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:14.605][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:14.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:14.609][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:14.610][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[2024-05-03 21:11:14.612][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-05-03 21:11:14.618][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:14.619][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:14.621][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-05-03 21:11:15.104][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-05-03 21:11:15.631][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:15.635][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-05-03 21:11:15.640][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-05-03 21:11:15.644][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-05-03 21:11:15.647][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 21:11:15.649][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 21:11:15.651][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 21:11:15.654][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:15.656][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:15.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:15.666][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:15.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:15.669][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:15.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:15.688][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:15.689][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:15.690][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.691][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:15.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:15.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:15.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:15.697][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:15.698][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:15.699][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.700][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:15.702][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:15.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:15.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:15.706][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:15.707][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:15.708][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.709][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:15.710][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:15.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:15.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:15.714][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:15.715][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:15.716][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.717][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:15.719][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:15.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:15.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:15.726][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:15.728][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:15.729][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.731][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:15.733][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:15.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:15.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:15.740][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:15.741][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:15.743][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.744][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:15.747][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:15.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:15.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:15.752][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:15.754][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:15.754][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.755][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:15.757][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:15.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:15.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:15.763][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:15.765][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:15.766][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.768][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:15.770][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:15.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:15.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:15.777][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:15.779][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:15.780][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.781][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:15.782][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:15.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:15.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:15.787][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:15.789][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:15.790][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.792][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:15.794][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:15.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:15.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:15.800][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:15.802][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:15.804][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.805][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:15.807][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:15.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:15.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:15.814][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:15.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:15.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:15.821][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:15.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:15.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:15.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:15.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:15.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:15.834][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:15.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:15.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:15.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:15.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:15.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:15.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:15.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:15.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:15.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:15.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:15.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:15.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:15.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:15.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:15.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:15.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:15.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:15.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:15.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:15.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:15.874][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-05-03 21:11:15.876][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:15.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:15.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:15.883][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:15.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:15.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:15.889][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:15.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:15.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:15.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:15.896][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:15.897][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:15.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:15.903][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:15.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:15.905][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:15.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:15.908][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-05-03 21:11:15.910][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 21:11:15.913][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-05-03 21:11:15.915][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 21:11:15.924][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 21:11:15.927][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 21:11:15.929][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 21:11:15.932][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 21:11:15.934][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 21:11:15.940][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:15.942][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:15.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:15.981][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:15.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:15.984][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:15.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:15.988][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-05-03 21:11:15.995][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:15.997][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:16.000][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-05-03 21:11:16.536][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-05-03 21:11:17.034][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:17.038][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-05-03 21:11:17.045][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-05-03 21:11:17.050][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-05-03 21:11:17.053][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 21:11:17.055][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 21:11:17.057][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 21:11:17.061][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:17.063][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:17.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:17.073][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:17.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:17.076][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:17.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:17.082][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:17.084][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:17.086][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:17.087][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:17.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:17.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:17.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:17.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:17.096][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:17.098][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:17.100][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:17.101][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:17.103][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:17.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:17.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:17.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:17.110][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:17.112][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:17.114][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:17.115][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:17.117][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:17.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:17.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:17.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:17.124][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:17.126][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:17.128][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:17.129][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:17.131][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:17.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:17.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:17.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:17.138][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:17.140][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:17.142][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:17.143][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:17.145][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:17.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:17.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:17.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:17.152][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:17.154][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:17.155][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:17.157][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:17.159][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:17.161][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:17.162][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:17.164][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:17.166][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:17.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:17.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:17.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:17.173][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:17.174][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:17.176][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:17.178][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:17.180][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:17.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:17.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:17.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:17.187][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:17.189][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:17.190][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:17.192][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:17.194][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:17.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:17.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:17.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:17.201][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:17.203][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:17.204][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:17.206][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:17.208][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:17.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:17.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:17.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:17.214][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:17.216][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:17.218][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:17.220][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:17.222][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:17.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:17.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:17.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:17.229][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:17.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:17.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:17.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:17.235][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:17.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:17.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:17.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:17.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:17.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:17.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:17.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:17.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:17.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:17.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:17.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:17.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:17.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:17.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:17.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:17.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:17.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:17.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:17.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:17.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:17.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:17.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:17.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:17.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:17.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:17.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:17.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:17.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:17.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:17.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:17.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:17.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:17.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:17.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:17.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:17.294][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-05-03 21:11:17.295][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:17.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:17.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:17.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:17.316][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:17.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:17.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:17.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:17.323][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:17.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:17.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:17.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:17.330][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:17.331][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:17.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:17.341][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:17.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:17.344][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:17.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:17.348][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-05-03 21:11:17.350][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 21:11:17.353][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-05-03 21:11:17.355][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 21:11:17.356][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 21:11:17.358][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 21:11:17.360][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 21:11:17.362][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 21:11:17.363][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 21:11:17.368][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:17.370][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:17.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:17.379][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:17.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:17.383][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:17.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:17.386][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-05-03 21:11:17.391][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:17.392][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:17.395][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-05-03 21:11:17.899][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-05-03 21:11:18.394][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:18.398][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-05-03 21:11:18.404][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-05-03 21:11:18.409][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-05-03 21:11:18.412][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 21:11:18.415][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 21:11:18.417][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 21:11:18.420][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:18.421][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:18.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:18.432][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:18.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:18.436][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:18.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:18.442][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:18.445][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:18.447][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:18.449][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:18.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:18.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:18.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:18.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:18.458][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:18.460][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:18.462][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:18.463][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:18.465][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:18.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:18.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:18.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:18.472][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:18.474][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:18.476][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:18.477][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:18.479][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:18.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:18.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:18.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:18.487][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:18.489][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:18.490][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:18.492][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:18.494][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:18.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:18.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:18.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:18.499][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:18.501][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:18.502][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:18.503][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:18.505][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:18.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:18.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:18.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:18.512][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:18.514][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:18.516][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:18.517][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:18.520][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:18.521][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:18.523][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:18.524][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:18.526][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:18.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:18.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:18.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:18.533][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:18.535][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:18.537][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:18.538][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:18.540][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:18.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:18.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:18.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:18.547][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:18.549][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:18.550][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:18.552][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:18.554][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:18.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:18.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:18.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:18.561][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:18.562][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:18.564][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:18.566][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:18.568][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:18.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:18.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:18.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:18.575][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:18.577][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:18.578][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:18.580][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:18.582][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:18.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:18.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:18.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:18.589][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:18.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:18.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:18.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:18.595][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:18.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:18.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:18.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:18.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:18.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:18.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:18.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:18.624][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:18.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:18.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:18.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:18.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:18.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:18.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:18.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:18.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:18.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:18.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:18.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:18.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:18.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:18.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:18.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:18.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:18.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:18.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:18.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:18.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:18.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:18.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:18.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:18.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:18.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:18.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:18.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:18.673][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-05-03 21:11:18.674][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:18.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:18.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:18.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:18.681][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:18.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:18.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:18.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:18.688][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:18.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:18.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:18.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:18.694][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:18.696][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:18.697][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:18.706][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:18.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:18.710][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:18.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:18.714][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-05-03 21:11:18.716][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 21:11:18.719][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-05-03 21:11:18.721][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 21:11:18.723][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 21:11:18.725][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 21:11:18.727][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 21:11:18.729][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 21:11:18.731][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 21:11:18.737][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:18.738][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:18.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:18.749][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:18.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:18.752][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:18.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:18.756][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-05-03 21:11:18.760][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:18.762][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:18.764][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-05-03 21:11:19.260][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-05-03 21:11:19.735][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:19.738][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-05-03 21:11:19.744][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-05-03 21:11:19.765][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-05-03 21:11:19.767][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 21:11:19.769][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 21:11:19.771][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 21:11:19.774][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:19.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:19.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:19.784][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:19.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:19.787][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:19.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:19.791][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:19.793][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:19.794][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:19.796][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:19.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:19.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:19.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:19.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:19.802][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:19.804][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:19.805][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:19.807][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:19.808][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:19.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:19.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:19.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:19.815][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:19.817][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:19.819][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:19.821][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:19.823][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:19.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:19.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:19.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:19.831][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:19.833][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:19.834][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:19.836][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:19.838][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:19.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:19.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:19.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:19.845][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:19.846][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:19.848][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:19.850][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:19.852][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:19.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:19.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:19.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:19.859][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:19.860][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:19.861][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:19.862][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:19.864][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:19.866][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:19.869][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:19.871][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:19.873][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:19.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:19.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:19.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:19.881][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:19.883][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:19.884][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:19.886][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:19.888][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:19.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:19.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:19.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:19.895][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:19.903][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:19.912][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:19.913][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:19.916][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:19.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:19.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:19.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:19.924][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:19.925][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:19.927][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:19.929][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:19.931][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:19.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:19.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:19.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:19.938][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:19.940][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:19.942][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:19.943][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:19.946][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:19.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:19.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:19.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:19.951][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:19.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:19.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:19.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:19.956][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:19.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:19.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:19.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:19.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:19.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:19.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:19.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:19.970][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:19.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:19.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:19.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:19.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:19.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:19.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:19.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:19.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:19.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:19.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:19.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:19.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:19.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:19.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:19.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:19.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:19.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:19.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:19.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:20.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:20.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:20.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:20.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:20.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:20.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:20.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:20.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:20.013][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-05-03 21:11:20.015][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:20.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:20.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:20.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:20.019][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:20.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:20.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:20.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:20.024][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:20.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:20.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:20.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:20.031][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:20.032][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:20.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:20.041][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:20.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:20.043][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:20.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:20.047][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-05-03 21:11:20.049][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 21:11:20.052][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-05-03 21:11:20.054][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 21:11:20.056][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 21:11:20.057][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 21:11:20.059][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 21:11:20.061][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 21:11:20.063][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 21:11:20.067][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:20.069][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:20.071][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:20.078][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:20.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:20.081][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:20.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:20.085][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-05-03 21:11:20.089][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:20.091][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:20.094][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-05-03 21:11:20.586][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-05-03 21:11:21.095][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:21.102][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-05-03 21:11:21.107][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-05-03 21:11:21.110][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-05-03 21:11:21.112][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 21:11:21.115][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 21:11:21.117][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 21:11:21.121][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:21.123][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:21.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:21.135][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:21.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:21.139][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:21.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:21.144][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:21.146][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:21.147][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:21.148][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:21.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:21.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:21.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:21.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:21.154][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:21.156][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:21.157][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:21.159][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:21.162][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:21.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:21.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:21.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:21.170][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:21.171][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:21.172][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:21.173][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:21.175][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:21.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:21.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:21.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:21.181][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:21.183][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:21.185][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:21.186][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:21.258][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:21.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:21.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:21.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:21.265][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:21.267][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:21.269][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:21.270][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:21.272][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:21.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:21.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:21.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:21.279][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:21.281][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:21.283][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:21.284][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:21.286][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:21.288][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:21.290][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:21.291][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:21.293][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:21.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:21.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:21.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:21.299][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:21.301][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:21.302][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:21.304][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:21.305][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:21.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:21.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:21.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:21.312][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:21.313][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:21.314][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:21.316][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:21.318][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:21.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:21.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:21.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:21.324][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:21.325][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:21.327][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:21.328][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:21.330][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:21.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:21.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:21.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:21.336][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:21.338][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:21.339][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:21.341][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:21.342][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:21.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:21.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:21.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:21.349][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:21.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:21.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:21.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:21.355][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:21.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:21.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:21.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:21.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:21.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:21.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:21.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:21.369][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:21.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:21.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:21.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:21.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:21.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:21.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:21.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:21.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:21.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:21.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:21.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:21.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:21.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:21.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:21.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:21.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:21.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:21.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:21.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:21.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:21.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:21.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:21.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:21.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:21.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:21.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:21.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:21.421][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-05-03 21:11:21.423][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:21.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:21.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:21.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:21.430][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:21.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:21.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:21.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:21.436][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:21.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:21.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:21.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:21.443][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:21.445][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:21.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:21.455][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:21.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:21.458][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:21.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:21.462][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-05-03 21:11:21.463][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 21:11:21.466][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-05-03 21:11:21.468][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 21:11:21.470][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 21:11:21.471][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 21:11:21.473][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 21:11:21.474][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 21:11:21.476][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 21:11:21.480][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:21.481][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:21.482][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:21.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:21.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:21.494][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:21.495][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[2024-05-03 21:11:21.497][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-05-03 21:11:21.501][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:21.503][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:21.505][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-05-03 21:11:21.990][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-05-03 21:11:22.490][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:22.494][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-05-03 21:11:22.499][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-05-03 21:11:22.502][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-05-03 21:11:22.504][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 21:11:22.505][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 21:11:22.507][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 21:11:22.510][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:22.512][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:22.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:22.520][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:22.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:22.530][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:22.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:22.539][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:22.540][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:22.542][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:22.544][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:22.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:22.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:22.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:22.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:22.554][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:22.556][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:22.557][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:22.559][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:22.561][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:22.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:22.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:22.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:22.569][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:22.571][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:22.573][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:22.575][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:22.577][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:22.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:22.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:22.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:22.582][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:22.584][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:22.585][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:22.586][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:22.587][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:22.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:22.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:22.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:22.591][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:22.592][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:22.593][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:22.595][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:22.597][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:22.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:22.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:22.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:22.602][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:22.603][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:22.604][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:22.605][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:22.607][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:22.609][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:22.610][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:22.612][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:22.614][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:22.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:22.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:22.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:22.620][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:22.622][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:22.623][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:22.625][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:22.627][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:22.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:22.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:22.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:22.632][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:22.633][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:22.634][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:22.635][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:22.636][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:22.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:22.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:22.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:22.640][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:22.642][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:22.643][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:22.644][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:22.645][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:22.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:22.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:22.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:22.650][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:22.651][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:22.652][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:22.653][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:22.655][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:22.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:22.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:22.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:22.659][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:22.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:22.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:22.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:22.662][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:22.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:22.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:22.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:22.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:22.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:22.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:22.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:22.670][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:22.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:22.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:22.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:22.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:22.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:22.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:22.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:22.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:22.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:22.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:22.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:22.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:22.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:22.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:22.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:22.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:22.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:22.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:22.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:22.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:22.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:22.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:22.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:22.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:22.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:22.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:22.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:22.697][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-05-03 21:11:22.698][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:22.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:22.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:22.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:22.702][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:22.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:22.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:22.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:22.706][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:22.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:22.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:22.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:22.710][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:22.711][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:22.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:22.716][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:22.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:22.718][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:22.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:22.720][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-05-03 21:11:22.721][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 21:11:22.723][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-05-03 21:11:22.724][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 21:11:22.725][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 21:11:22.726][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 21:11:22.727][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 21:11:22.728][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 21:11:22.729][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 21:11:22.731][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:22.732][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:22.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:22.738][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:22.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:22.745][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:22.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:22.748][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-05-03 21:11:22.750][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:22.751][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:22.753][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-05-03 21:11:23.241][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-05-03 21:11:23.747][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:23.751][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-05-03 21:11:23.757][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-05-03 21:11:23.761][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-05-03 21:11:23.764][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 21:11:23.765][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 21:11:23.767][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 21:11:23.770][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:23.772][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:23.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:23.782][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:23.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:23.786][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:23.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:23.791][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:23.792][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:23.794][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:23.796][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:23.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:23.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:23.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:23.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:23.803][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:23.805][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:23.807][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:23.808][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:23.810][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:23.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:23.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:23.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:23.816][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:23.818][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:23.819][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:23.821][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:23.822][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:23.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:23.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:23.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:23.829][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:23.830][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:23.832][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:23.833][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:23.835][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:23.837][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:23.838][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:23.840][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:23.842][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:23.843][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:23.845][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:23.846][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:23.848][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:23.850][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:23.851][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:23.853][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:23.854][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:23.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:23.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:23.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:23.861][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:23.863][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:23.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:23.866][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:23.868][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:23.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:23.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:23.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:23.875][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:23.876][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:23.878][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:23.879][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:23.882][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:23.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:23.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:23.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:23.889][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:23.890][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:23.892][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:23.894][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:23.896][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:23.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:23.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:23.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:23.902][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:23.903][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:23.905][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:23.906][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:23.908][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:23.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:23.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:23.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:23.915][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:23.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:23.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:23.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:23.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:23.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:23.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:23.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:23.928][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:23.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:23.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:23.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:23.935][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:23.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:23.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:23.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:23.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:23.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:23.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:23.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:23.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:23.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:23.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:23.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:23.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:23.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:23.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:23.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:23.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:23.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:23.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:23.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:23.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:23.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:23.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:23.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:23.974][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-05-03 21:11:23.975][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:23.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:23.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:23.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:23.981][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:23.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:23.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:23.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:23.986][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:23.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:23.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:23.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:23.993][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:23.994][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:23.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:24.069][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:24.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:24.073][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:24.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:24.093][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-05-03 21:11:24.095][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 21:11:24.098][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-05-03 21:11:24.100][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 21:11:24.102][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 21:11:24.105][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 21:11:24.106][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 21:11:24.109][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 21:11:24.110][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 21:11:24.115][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:24.117][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:24.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:24.128][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:24.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:24.132][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:24.134][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[2024-05-03 21:11:24.136][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-05-03 21:11:24.141][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:24.143][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:24.146][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-05-03 21:11:24.657][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2024-05-03 21:11:25.161][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:25.165][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-05-03 21:11:25.171][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-05-03 21:11:25.175][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-05-03 21:11:25.178][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 21:11:25.181][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 21:11:25.183][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 21:11:25.186][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:25.187][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:25.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:25.196][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:25.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:25.199][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:25.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:25.204][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:25.205][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:25.207][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:25.208][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:25.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:25.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:25.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:25.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:25.217][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:25.219][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:25.220][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:25.222][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:25.224][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:25.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:25.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:25.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:25.230][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:25.232][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:25.234][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:25.235][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:25.237][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:25.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:25.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:25.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:25.243][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:25.244][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:25.245][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:25.246][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:25.247][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:25.248][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:25.249][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:25.250][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:25.251][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:25.252][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:25.254][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:25.255][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:25.257][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:25.258][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:25.260][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:25.261][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:25.263][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:25.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:25.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:25.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:25.268][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:25.270][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:25.271][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:25.273][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:25.275][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:25.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:25.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:25.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:25.280][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:25.281][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:25.282][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:25.283][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:25.285][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:25.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:25.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:25.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:25.291][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:25.292][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:25.294][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:25.295][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:25.297][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:25.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:25.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:25.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:25.304][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:25.305][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:25.306][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:25.307][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:25.309][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:25.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:25.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:25.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:25.313][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:25.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:25.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:25.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:25.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:25.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:25.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:25.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:25.326][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:25.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:25.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:25.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:25.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:25.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:25.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:25.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:25.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:25.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:25.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:25.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:25.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:25.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:25.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:25.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:25.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:25.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:25.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:25.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:25.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:25.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:25.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:25.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:25.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:25.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:25.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:25.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:25.373][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-05-03 21:11:25.375][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:25.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:25.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:25.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:25.393][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:25.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:25.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:25.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:25.400][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:25.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:25.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:25.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:25.406][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:25.407][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:25.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:25.413][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:25.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:25.415][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:25.416][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[2024-05-03 21:11:25.418][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-05-03 21:11:25.419][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 21:11:25.421][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-05-03 21:11:25.422][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 21:11:25.424][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 21:11:25.426][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 21:11:25.428][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 21:11:25.430][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 21:11:25.432][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 21:11:25.437][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:25.438][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:25.440][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:25.449][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:25.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:25.453][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:25.455][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[2024-05-03 21:11:25.456][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-05-03 21:11:25.459][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:25.460][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:25.462][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-05-03 21:11:25.954][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2024-05-03 21:11:26.448][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:26.452][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-05-03 21:11:26.458][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-05-03 21:11:26.464][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-05-03 21:11:26.466][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 21:11:26.467][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 21:11:26.468][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 21:11:26.470][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:26.471][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:26.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:26.481][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:26.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:26.483][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:26.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:26.488][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:26.490][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:26.492][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:26.493][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:26.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:26.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:26.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:26.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:26.503][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:26.505][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:26.506][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:26.507][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:26.509][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:26.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:26.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:26.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:26.513][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:26.514][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:26.515][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:26.516][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:26.518][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:26.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:26.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:26.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:26.522][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:26.523][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:26.525][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:26.526][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:26.528][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:26.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:26.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:26.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:26.533][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:26.534][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:26.535][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:26.536][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:26.537][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:26.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:26.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:26.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:26.541][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:26.542][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:26.543][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:26.544][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:26.546][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:26.547][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:26.549][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:26.551][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:26.553][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:26.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:26.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:26.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:26.559][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:26.561][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:26.563][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:26.564][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:26.566][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:26.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:26.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:26.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:26.572][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:26.574][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:26.575][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:26.577][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:26.580][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:26.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:26.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:26.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:26.587][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:26.588][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:26.589][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:26.590][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:26.591][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:26.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:26.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:26.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:26.596][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:26.597][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:26.598][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:26.598][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:26.600][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:26.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:26.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:26.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:26.606][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:26.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:26.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:26.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:26.612][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:26.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:26.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:26.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:26.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:26.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:26.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:26.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:26.674][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:26.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:26.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:26.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:26.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:26.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:26.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:26.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:26.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:26.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:26.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:26.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:26.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:26.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:26.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:26.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:26.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:26.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:26.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:26.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:26.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:26.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:26.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:26.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:26.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:26.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:26.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:26.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:26.706][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-05-03 21:11:26.707][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:26.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:26.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:26.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:26.711][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:26.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:26.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:26.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:26.715][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:26.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:26.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:26.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:26.719][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:26.720][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:26.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:26.726][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:26.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:26.727][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:26.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:26.729][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-05-03 21:11:26.731][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 21:11:26.732][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-05-03 21:11:26.734][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 21:11:26.735][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 21:11:26.736][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 21:11:26.737][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 21:11:26.738][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 21:11:26.739][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 21:11:26.742][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:26.742][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:26.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:26.748][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:26.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:26.750][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:26.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:26.752][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-05-03 21:11:26.755][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:26.756][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:26.757][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-05-03 21:11:27.219][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-05-03 21:11:27.716][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:27.719][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-05-03 21:11:27.722][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-05-03 21:11:27.725][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-05-03 21:11:27.726][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 21:11:27.728][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 21:11:27.729][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 21:11:27.731][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:27.732][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:27.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:27.737][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:27.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:27.739][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:27.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:27.743][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:27.744][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:27.745][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:27.746][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:27.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:27.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:27.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:27.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:27.752][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:27.753][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:27.754][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:27.755][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:27.756][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:27.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:27.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:27.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:27.761][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:27.762][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:27.763][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:27.764][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:27.766][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:27.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:27.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:27.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:27.770][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:27.771][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:27.772][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:27.773][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:27.775][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:27.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:27.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:27.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:27.779][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:27.780][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:27.781][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:27.782][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:27.783][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:27.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:27.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:27.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:27.787][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:27.788][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:27.789][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:27.790][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:27.792][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:27.793][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:27.794][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:27.795][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:27.796][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:27.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:27.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:27.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:27.800][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:27.801][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:27.802][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:27.803][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:27.804][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:27.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:27.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:27.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:27.808][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:27.809][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:27.810][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:27.811][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:27.817][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:27.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:27.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:27.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:27.825][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:27.826][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:27.827][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:27.828][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:27.829][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:27.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:27.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:27.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:27.833][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:27.834][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:27.834][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:27.835][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:27.837][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:27.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:27.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:27.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:27.841][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:27.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:27.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:27.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:27.844][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:27.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:27.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:27.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:27.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:27.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:27.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:27.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:27.852][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:27.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:27.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:27.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:27.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:27.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:27.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:27.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:27.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:27.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:27.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:27.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:27.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:27.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:27.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:27.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:27.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:27.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:27.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:27.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:27.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:27.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:27.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:27.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:27.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:27.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:27.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:27.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:27.878][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-05-03 21:11:27.879][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:27.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:27.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:27.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:27.883][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:27.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:27.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:27.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:27.887][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:27.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:27.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:27.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:27.891][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:27.892][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:27.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:27.897][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:27.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:27.899][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:27.900][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[2024-05-03 21:11:27.901][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-05-03 21:11:27.902][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 21:11:27.903][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-05-03 21:11:27.905][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 21:11:27.906][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 21:11:27.907][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 21:11:27.908][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 21:11:27.909][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 21:11:27.910][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 21:11:27.912][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:27.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:27.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:27.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:27.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:27.920][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:27.921][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[2024-05-03 21:11:27.922][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-05-03 21:11:27.924][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:27.925][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:27.927][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-05-03 21:11:28.389][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-05-03 21:11:28.895][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:28.900][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-05-03 21:11:28.907][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-05-03 21:11:28.912][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-05-03 21:11:28.916][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 21:11:28.918][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 21:11:28.921][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 21:11:28.924][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:28.926][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:28.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:28.938][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:28.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:28.942][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:28.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:28.947][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:28.949][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:28.951][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:28.952][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:28.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:28.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:28.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:28.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:28.960][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:28.962][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:28.963][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:28.964][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:28.966][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:28.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:28.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:28.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:28.971][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:28.972][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:28.973][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:28.975][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:28.976][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:28.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:28.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:28.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:28.981][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:28.982][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:28.983][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:28.984][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:28.985][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:28.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:28.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:28.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:28.989][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:28.998][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:28.999][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:29.000][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:29.001][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:29.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:29.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:29.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:29.005][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:29.006][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:29.007][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:29.008][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:29.009][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:29.010][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:29.011][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:29.012][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:29.013][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:29.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:29.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:29.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:29.017][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:29.018][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:29.019][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:29.020][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:29.021][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:29.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:29.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:29.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:29.025][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:29.026][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:29.026][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:29.027][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:29.029][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:29.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:29.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:29.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:29.032][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:29.033][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:29.034][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:29.035][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:29.036][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:29.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:29.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:29.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:29.040][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:29.041][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:29.042][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:29.043][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:29.044][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:29.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:29.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:29.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:29.048][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:29.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:29.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:29.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:29.051][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:29.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:29.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:29.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:29.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:29.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:29.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:29.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:29.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:29.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:29.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:29.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:29.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:29.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:29.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:29.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:29.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:29.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:29.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:29.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:29.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:29.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:29.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:29.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:29.075][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:29.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:29.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:29.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:29.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:29.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:29.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:29.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:29.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:29.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:29.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:29.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:29.086][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-05-03 21:11:29.087][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:29.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:29.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:29.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:29.091][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:29.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:29.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:29.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:29.095][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:29.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:29.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:29.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:29.099][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:29.099][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:29.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:29.105][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:29.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:29.106][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:29.107][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[2024-05-03 21:11:29.108][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-05-03 21:11:29.109][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 21:11:29.111][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-05-03 21:11:29.112][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 21:11:29.113][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 21:11:29.114][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 21:11:29.115][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 21:11:29.116][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 21:11:29.117][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 21:11:29.119][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:29.120][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:29.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:29.125][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:29.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:29.127][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:29.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:29.129][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-05-03 21:11:29.132][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:29.133][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:29.134][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-05-03 21:11:29.593][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-05-03 21:11:30.101][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:30.104][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-05-03 21:11:30.110][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-05-03 21:11:30.114][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-05-03 21:11:30.116][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 21:11:30.118][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 21:11:30.120][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 21:11:30.123][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:30.124][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:30.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:30.133][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:30.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:30.136][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:30.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:30.140][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:30.154][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:30.156][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:30.157][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:30.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:30.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:30.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:30.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:30.165][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:30.166][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:30.168][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:30.169][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:30.170][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:30.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:30.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:30.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:30.176][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:30.178][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:30.179][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:30.180][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:30.181][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:30.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:30.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:30.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:30.187][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:30.188][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:30.190][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:30.191][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:30.193][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:30.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:30.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:30.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:30.197][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:30.199][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:30.200][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:30.201][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:30.203][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:30.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:30.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:30.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:30.208][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:30.210][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:30.211][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:30.213][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:30.214][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:30.215][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:30.216][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:30.217][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:30.218][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:30.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:30.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:30.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:30.222][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:30.223][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:30.224][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:30.225][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:30.226][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:30.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:30.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:30.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:30.230][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:30.231][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:30.232][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:30.233][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:30.234][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:30.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:30.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:30.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:30.238][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:30.239][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:30.240][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:30.241][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:30.242][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:30.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:30.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:30.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:30.246][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:30.247][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:30.247][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:30.248][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:30.250][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:30.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:30.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:30.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:30.253][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:30.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:30.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:30.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:30.257][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:30.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:30.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:30.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:30.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:30.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:30.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:30.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:30.265][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:30.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:30.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:30.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:30.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:30.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:30.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:30.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:30.272][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:30.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:30.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:30.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:30.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:30.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:30.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:30.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:30.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:30.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:30.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:30.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:30.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:30.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:30.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:30.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:30.287][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:30.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:30.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:30.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:30.291][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-05-03 21:11:30.292][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:30.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:30.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:30.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:30.296][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:30.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:30.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:30.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:30.299][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:30.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:30.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:30.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:30.303][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:30.304][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:30.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:30.309][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:30.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:30.311][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:30.311][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.DEBUG[2024-05-03 21:11:30.312][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-05-03 21:11:30.313][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 21:11:30.315][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-05-03 21:11:30.316][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 21:11:30.318][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 21:11:30.319][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 21:11:30.321][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 21:11:30.322][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 21:11:30.323][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 21:11:30.327][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:30.329][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:30.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:30.337][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:30.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:30.340][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:30.341][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[2024-05-03 21:11:30.350][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-05-03 21:11:30.354][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:30.355][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:30.358][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-05-03 21:11:30.830][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-05-03 21:11:31.287][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:31.289][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-05-03 21:11:31.292][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-05-03 21:11:31.295][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-05-03 21:11:31.296][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 21:11:31.297][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 21:11:31.298][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 21:11:31.300][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:31.300][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:31.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:31.305][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:31.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:31.307][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:31.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:31.310][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:31.311][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:31.312][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:31.313][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:31.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:31.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:31.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:31.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:31.318][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:31.319][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:31.320][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:31.321][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:31.322][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:31.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:31.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:31.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:31.325][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:31.326][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:31.327][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:31.328][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:31.329][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:31.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:31.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:31.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:31.333][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:31.334][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:31.335][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:31.336][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:31.337][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:31.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:31.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:31.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:31.341][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:31.342][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:31.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:31.343][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:31.344][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:31.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:31.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:31.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:31.348][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:31.349][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:31.350][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:31.351][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:31.352][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:31.353][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:31.354][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:31.355][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:31.356][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:31.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:31.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:31.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:31.360][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:31.361][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:31.361][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:31.362][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:31.363][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:31.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:31.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:31.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:31.367][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:31.368][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:31.369][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:31.370][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:31.371][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:31.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:31.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:31.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:31.375][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:31.376][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:31.377][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:31.377][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:31.379][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:31.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:31.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:31.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:31.382][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:31.383][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:31.384][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:31.385][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:31.386][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:31.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:31.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:31.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:31.390][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:31.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:31.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:31.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:31.394][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:31.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:31.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:31.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:31.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:31.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:31.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:31.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:31.401][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:31.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:31.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:31.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:31.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:31.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:31.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:31.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:31.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:31.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:31.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:31.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:31.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:31.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:31.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:31.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:31.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:31.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:31.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:31.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:31.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:31.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:31.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:31.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:31.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:31.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:31.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:31.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:31.427][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-05-03 21:11:31.428][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:31.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:31.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:31.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:31.431][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:31.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:31.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:31.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:31.435][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:31.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:31.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:31.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:31.446][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:31.447][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:31.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:31.452][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:31.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:31.454][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:31.455][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[2024-05-03 21:11:31.456][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-05-03 21:11:31.457][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 21:11:31.458][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-05-03 21:11:31.459][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 21:11:31.460][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 21:11:31.461][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 21:11:31.462][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 21:11:31.463][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 21:11:31.464][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 21:11:31.467][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:31.468][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:31.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:31.473][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:31.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:31.474][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:31.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:31.476][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-05-03 21:11:31.479][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:31.480][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:31.481][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-05-03 21:11:31.939][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-05-03 21:11:32.402][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:32.404][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-05-03 21:11:32.407][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-05-03 21:11:32.410][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-05-03 21:11:32.411][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 21:11:32.412][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 21:11:32.414][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 21:11:32.415][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:32.416][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:32.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:32.422][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:32.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:32.424][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:32.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:32.428][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:32.429][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:32.430][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:32.431][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:32.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:32.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:32.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:32.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:32.437][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:32.438][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:32.439][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:32.440][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:32.441][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:32.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:32.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:32.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:32.445][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:32.446][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:32.447][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:32.448][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:32.450][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:32.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:32.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:32.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:32.454][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:32.455][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:32.456][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:32.457][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:32.458][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:32.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:32.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:32.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:32.462][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:32.463][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:32.464][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:32.465][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:32.467][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:32.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:32.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:32.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:32.471][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:32.472][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:32.473][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:32.473][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:32.475][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:32.476][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:32.477][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:32.477][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:32.479][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:32.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:32.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:32.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:32.483][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:32.484][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:32.485][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:32.486][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:32.487][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:32.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:32.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:32.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:32.491][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:32.492][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:32.493][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:32.494][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:32.495][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:32.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:32.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:32.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:32.499][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:32.500][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:32.501][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:32.502][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:32.503][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:32.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:32.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:32.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:32.507][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:32.508][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:32.509][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:32.510][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:32.511][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:32.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:32.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:32.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:32.515][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:32.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:32.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:32.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:32.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:32.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:32.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:32.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:32.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:32.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:32.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:32.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:32.526][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:32.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:32.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:32.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:32.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:32.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:32.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:32.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:32.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:32.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:32.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:32.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:32.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:32.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:32.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:32.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:32.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:32.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:32.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:32.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:32.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:32.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:32.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:32.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:32.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:32.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:32.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:32.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:32.564][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-05-03 21:11:32.565][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:32.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:32.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:32.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:32.569][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:32.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:32.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:32.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:32.572][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:32.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:32.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:32.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:32.576][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:32.577][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:32.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:32.582][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:32.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:32.584][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:32.585][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[2024-05-03 21:11:32.586][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-05-03 21:11:32.587][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 21:11:32.589][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-05-03 21:11:32.590][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 21:11:32.591][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 21:11:32.592][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 21:11:32.593][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 21:11:32.594][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 21:11:32.595][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 21:11:32.597][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:32.598][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:32.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:32.603][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:32.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:32.605][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:32.606][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[2024-05-03 21:11:32.607][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2024-05-03 21:11:32.610][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:32.611][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:32.612][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-05-03 21:11:33.075][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-05-03 21:11:33.531][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:33.533][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-05-03 21:11:33.536][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-05-03 21:11:33.538][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-05-03 21:11:33.539][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 21:11:33.541][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 21:11:33.542][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 21:11:33.543][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:33.544][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:33.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:33.549][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:33.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:33.551][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:33.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:33.554][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:33.555][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:33.555][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.556][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:33.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:33.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.561][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:33.562][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:33.563][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.564][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.565][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:33.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:33.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.569][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:33.570][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:33.571][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.571][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.573][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:33.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:33.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.577][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:33.578][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:33.578][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.579][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.580][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:33.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:33.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.584][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:33.585][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:33.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.587][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.588][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:33.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:33.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.592][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:33.593][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:33.594][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.594][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.596][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:33.597][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.597][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.598][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.599][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:33.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.603][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:33.604][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:33.605][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.606][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.607][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:33.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:33.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.611][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:33.612][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:33.613][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.613][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.615][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:33.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:33.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.623][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:33.628][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:33.629][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.630][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.631][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:33.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:33.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.635][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:33.635][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:33.636][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.637][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.638][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:33.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:33.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.642][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:33.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:33.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.646][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:33.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:33.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:33.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:33.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.653][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:33.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:33.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:33.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:33.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:33.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:33.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:33.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:33.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:33.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:33.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:33.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:33.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:33.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:33.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:33.679][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-05-03 21:11:33.680][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.684][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.687][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:33.706][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[2024-05-03 21:11:33.709][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 21:11:33.711][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-03 21:11:33.712][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 21:11:33.713][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-05-03 21:11:33.716][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:33.717][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:33.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:33.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:33.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:33.723][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:33.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:33.725][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.729][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.732][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:33.736][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:33.737][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:33.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:33.742][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:33.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:33.744][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:33.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:33.746][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.749][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.753][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.757][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.761][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:33.765][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:33.765][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:33.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:33.770][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:33.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:33.772][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:33.773][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[2024-05-03 21:11:33.774][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.778][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.781][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.790][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.794][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:33.798][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:33.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:33.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:33.803][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:33.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:33.805][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:33.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:33.807][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.811][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.815][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.818][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.822][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:33.826][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:33.826][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:33.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:33.832][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:33.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:33.833][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:33.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:33.835][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.839][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.842][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:33.846][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:33.847][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:33.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:33.852][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:33.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:33.854][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:33.855][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.TRACE[2024-05-03 21:11:33.856][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.860][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.863][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:33.867][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:33.868][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:33.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:33.873][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:33.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:33.874][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:33.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:33.876][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.880][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.884][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:33.887][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:33.888][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:33.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:33.893][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:33.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:33.895][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:33.896][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[2024-05-03 21:11:33.897][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.901][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.904][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:33.908][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:33.909][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:33.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:33.914][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:33.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:33.916][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:33.917][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[2024-05-03 21:11:33.918][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.921][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.925][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:33.929][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:33.930][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:33.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:33.935][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:33.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:33.937][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:33.937][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[2024-05-03 21:11:33.938][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.942][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.946][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:33.954][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:33.955][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:33.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:33.960][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:33.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:33.962][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:33.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:33.964][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.967][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.971][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:33.975][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:33.976][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:33.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:33.981][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:33.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:33.982][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:33.983][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.TRACE[2024-05-03 21:11:33.984][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.988][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:33.992][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:33.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:33.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:33.995][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:33.996][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:33.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:34.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:34.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:34.003][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:34.004][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.TRACE[2024-05-03 21:11:34.005][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:34.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:34.009][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:34.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:34.012][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:34.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:34.016][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:34.017][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:34.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:34.022][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:34.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:34.024][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:34.024][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.TRACE[2024-05-03 21:11:34.025][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:34.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:34.029][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:34.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:34.033][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:34.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:34.036][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:34.037][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:34.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:34.042][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:34.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:34.044][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:34.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:34.046][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:34.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:34.050][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:34.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:34.053][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:34.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:34.057][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:34.058][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:34.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:34.063][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:34.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:34.064][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:34.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:34.066][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:34.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:34.070][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:34.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:34.074][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:34.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:34.078][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:34.078][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:34.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:34.083][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:34.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:34.085][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:34.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:34.087][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:34.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:34.091][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:34.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:34.095][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:34.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:34.098][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:34.099][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:34.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:34.104][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:34.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:34.106][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:34.107][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.TRACE[2024-05-03 21:11:34.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:34.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:34.116][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:34.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:34.120][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:34.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:34.124][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:34.125][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:34.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:34.130][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:34.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:34.131][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:34.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:34.133][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:34.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:34.137][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:34.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:34.141][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:34.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:34.144][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:34.145][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:34.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:34.150][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:34.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:34.152][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:34.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:34.154][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:34.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:34.158][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:34.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:34.162][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:34.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:34.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:34.177][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:34.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:34.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:34.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:34.181][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:34.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:34.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:34.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:34.185][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:34.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:34.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:34.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:34.189][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:34.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:34.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:34.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:34.192][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:34.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:34.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:34.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:34.220][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[2024-05-03 21:11:34.223][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:34.224][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:34.226][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-05-03 21:11:34.686][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-05-03 21:11:35.180][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:35.184][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2024-05-03 21:11:35.192][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2024-05-03 21:11:35.199][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-03 21:11:35.214][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:35.218][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:35.223][private$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[2024-05-03 21:11:35.714][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[2024-05-03 21:11:36.176][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:36.178][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2024-05-03 21:11:36.183][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2024-05-03 21:11:36.187][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:36.188][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:36.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:36.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:36.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:36.197][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:36.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:36.199][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-05-03 21:11:36.200][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 21:11:36.202][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-05-03 21:11:36.203][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 21:11:36.218][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 21:11:36.225][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 21:11:36.227][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 21:11:36.228][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 21:11:36.229][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 21:11:36.232][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:36.233][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:36.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:36.238][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:36.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:36.240][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:36.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:36.242][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2024-05-03 21:11:36.245][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:36.246][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:36.247][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2024-05-03 21:11:36.702][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2024-05-03 21:11:37.178][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:37.183][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2024-05-03 21:11:37.191][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2024-05-03 21:11:37.196][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2024-05-03 21:11:37.200][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 21:11:37.203][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 21:11:37.205][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 21:11:37.209][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:37.211][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:37.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:37.223][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:37.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:37.226][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:37.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:37.232][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:37.234][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:37.235][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.237][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:37.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:37.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.245][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:37.246][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:37.248][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.249][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.251][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:37.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:37.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.256][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:37.257][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:37.258][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.259][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.261][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:37.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:37.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.266][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:37.267][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:37.268][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.269][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.270][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:37.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:37.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.274][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:37.275][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:37.276][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.277][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.278][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:37.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:37.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.282][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:37.284][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:37.284][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.285][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.287][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:37.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:37.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.291][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:37.292][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:37.293][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.294][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.295][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:37.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:37.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.299][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:37.300][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:37.301][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.302][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.303][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:37.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:37.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.307][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:37.308][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:37.309][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.310][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.311][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:37.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:37.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.315][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:37.316][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:37.317][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.318][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.319][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:37.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:37.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.323][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:37.324][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:37.325][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.326][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.327][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:37.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:37.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.331][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:37.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:37.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.335][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:37.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:37.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:37.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:37.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.342][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:37.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:37.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:37.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:37.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:37.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:37.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:37.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:37.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:37.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:37.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:37.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:37.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:37.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:37.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:37.376][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-05-03 21:11:37.377][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:37.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:37.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.381][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:37.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:37.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.385][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:37.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:37.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:37.388][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:37.389][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:37.390][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:37.394][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:37.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:37.396][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:37.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:37.398][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:37.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:37.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.401][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:37.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:37.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:37.405][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:37.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:37.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:37.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:37.409][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:37.410][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:37.410][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:37.415][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:37.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:37.416][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:37.417][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.DEBUG[2024-05-03 21:11:37.418][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-05-03 21:11:37.419][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 21:11:37.421][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-05-03 21:11:37.422][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 21:11:37.423][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 21:11:37.424][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 21:11:37.425][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 21:11:37.426][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 21:11:37.427][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 21:11:37.429][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:37.430][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:37.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:37.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:37.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:37.437][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:37.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:37.438][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2024-05-03 21:11:37.441][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:37.442][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:37.443][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2024-05-03 21:11:37.902][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2024-05-03 21:11:38.409][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:38.411][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2024-05-03 21:11:38.414][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2024-05-03 21:11:38.417][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2024-05-03 21:11:38.418][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 21:11:38.419][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 21:11:38.420][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 21:11:38.422][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:38.423][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:38.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:38.428][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:38.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:38.430][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:38.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:38.433][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:38.434][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:38.435][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.436][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:38.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:38.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.441][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:38.442][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:38.443][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.444][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.445][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:38.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:38.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.450][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:38.451][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:38.452][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.453][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.454][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:38.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:38.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.458][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:38.459][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:38.460][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.461][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.462][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:38.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:38.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.466][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:38.467][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:38.468][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.469][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.470][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:38.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:38.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.474][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:38.475][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:38.476][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.477][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.478][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:38.479][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:38.480][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.481][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.482][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:38.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:38.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.486][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.487][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.487][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.488][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.489][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.502][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:38.503][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:38.503][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.504][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.506][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:38.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:38.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.509][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:38.510][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:38.511][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.512][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.513][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:38.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:38.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.517][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:38.518][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:38.519][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.520][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.521][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:38.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:38.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.525][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:38.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:38.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.529][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:38.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:38.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:38.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:38.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.536][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:38.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:38.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:38.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:38.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:38.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:38.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:38.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:38.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:38.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:38.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:38.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:38.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:38.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:38.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:38.562][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-05-03 21:11:38.563][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.567][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.571][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:38.590][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[2024-05-03 21:11:38.593][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 21:11:38.594][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-03 21:11:38.595][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 21:11:38.597][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-05-03 21:11:38.599][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:38.600][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:38.601][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:38.605][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:38.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:38.606][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:38.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:38.608][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.612][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.615][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:38.619][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:38.620][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:38.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:38.625][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:38.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:38.627][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:38.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:38.628][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.632][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.636][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.640][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.643][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:38.647][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:38.648][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:38.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:38.653][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:38.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:38.654][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:38.655][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[2024-05-03 21:11:38.661][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.665][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.669][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.672][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.676][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:38.680][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:38.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:38.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:38.686][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:38.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:38.687][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:38.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:38.689][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.693][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.697][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.700][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:38.708][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:38.709][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:38.709][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:38.713][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:38.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:38.715][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:38.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:38.717][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.721][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.724][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:38.728][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:38.729][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:38.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:38.734][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:38.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:38.735][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:38.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:38.737][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.741][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.744][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:38.748][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:38.749][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:38.750][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:38.754][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:38.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:38.755][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:38.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:38.757][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.761][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.765][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:38.768][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:38.769][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:38.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:38.774][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:38.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:38.776][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:38.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:38.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.781][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.785][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:38.789][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:38.789][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:38.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:38.794][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:38.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:38.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:38.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:38.798][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.801][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.805][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:38.809][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:38.810][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:38.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:38.814][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:38.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:38.821][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:38.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:38.822][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.826][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:38.833][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:38.834][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:38.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:38.839][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:38.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:38.841][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:38.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:38.843][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.846][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.850][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:38.853][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:38.854][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:38.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:38.859][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:38.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:38.861][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:38.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:38.863][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.866][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.870][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:38.873][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:38.874][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:38.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:38.879][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:38.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:38.881][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:38.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:38.883][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.886][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.890][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:38.893][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:38.894][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:38.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:38.899][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:38.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:38.901][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:38.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:38.903][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.906][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.910][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:38.914][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:38.914][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:38.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:38.919][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:38.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:38.921][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:38.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:38.923][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.926][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.930][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:38.934][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:38.935][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:38.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:38.940][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:38.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:38.941][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:38.942][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.TRACE[2024-05-03 21:11:38.943][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.947][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.950][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:38.954][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:38.955][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:38.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:38.960][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:38.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:38.961][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:38.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:38.963][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.967][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.970][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:38.981][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:38.982][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:38.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:38.987][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:38.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:38.989][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:38.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:38.991][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.995][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:38.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:38.998][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:38.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:39.002][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:39.003][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:39.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:39.008][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:39.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:39.009][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:39.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:39.011][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.015][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.018][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:39.022][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:39.023][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:39.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:39.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:39.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:39.029][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:39.030][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.TRACE[2024-05-03 21:11:39.031][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.035][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.038][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:39.057][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[2024-05-03 21:11:39.059][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 21:11:39.061][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-03 21:11:39.062][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 21:11:39.063][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-05-03 21:11:39.066][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:39.066][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:39.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:39.071][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:39.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:39.073][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:39.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:39.075][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.078][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.082][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:39.086][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:39.086][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:39.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:39.091][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:39.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:39.093][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:39.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:39.095][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.098][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.102][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.106][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.109][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:39.113][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:39.114][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:39.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:39.119][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:39.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:39.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:39.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:39.122][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.126][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.130][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.133][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.142][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:39.146][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:39.147][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:39.147][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:39.152][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:39.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:39.153][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:39.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:39.155][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.159][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.162][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.166][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.170][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:39.173][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:39.174][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:39.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:39.179][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:39.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:39.181][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:39.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:39.183][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.186][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.190][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:39.194][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:39.194][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:39.195][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:39.199][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:39.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:39.201][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:39.202][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[2024-05-03 21:11:39.203][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.206][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.210][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:39.214][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:39.214][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:39.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:39.219][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:39.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:39.221][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:39.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:39.223][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.226][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.230][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:39.234][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:39.234][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:39.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:39.239][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:39.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:39.241][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:39.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:39.243][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.246][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.250][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:39.254][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:39.255][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:39.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:39.260][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:39.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:39.261][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:39.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:39.263][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.267][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.270][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:39.274][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:39.275][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:39.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:39.280][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:39.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:39.281][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:39.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:39.283][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.287][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.291][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:39.294][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:39.295][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:39.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:39.305][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:39.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:39.306][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:39.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:39.308][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.312][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.316][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:39.319][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:39.320][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:39.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:39.325][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:39.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:39.327][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:39.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:39.328][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.332][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.336][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:39.339][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:39.340][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:39.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:39.345][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:39.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:39.346][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:39.347][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.TRACE[2024-05-03 21:11:39.348][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.352][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.356][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:39.359][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:39.360][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:39.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:39.365][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:39.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:39.366][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:39.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:39.368][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.372][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.376][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:39.379][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:39.380][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:39.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:39.385][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:39.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:39.386][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:39.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:39.388][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.392][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.396][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:39.399][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:39.400][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:39.401][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:39.405][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:39.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:39.407][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:39.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:39.409][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.412][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.416][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:39.420][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:39.421][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:39.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:39.425][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:39.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:39.427][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:39.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:39.429][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.433][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.436][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:39.440][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:39.441][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:39.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:39.445][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:39.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:39.447][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:39.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:39.449][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.452][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.461][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:39.465][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:39.465][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:39.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:39.470][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:39.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:39.472][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:39.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:39.474][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.478][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.481][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:39.485][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:39.486][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:39.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:39.491][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:39.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:39.492][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:39.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:39.494][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.498][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.502][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.517][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-03 21:11:39.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-03 21:11:39.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-03 21:11:39.526][biodb::testThat]
biodb.INFO [2024-05-03 21:11:39.527][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-05-03 21:11:39.528][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 21:11:39.529][biodb::testThat]
biodb.TRACE[2024-05-03 21:11:39.532][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-03 21:11:39.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-03 21:11:39.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.536][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:39.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:39.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.539][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:39.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:39.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.543][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:39.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:39.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.547][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:39.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:39.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:39.553][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:39.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:39.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:39.559][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:39.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:39.561][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:39.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:39.564][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[2024-05-03 21:11:39.567][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 21:11:39.568][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-05-03 21:11:39.569][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 21:11:39.571][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-05-03 21:11:39.573][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:39.574][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:39.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:39.579][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:39.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:39.580][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:39.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:39.582][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:39.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:39.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.586][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:39.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:39.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.589][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:39.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:39.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:39.594][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[2024-05-03 21:11:39.597][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 21:11:39.598][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-05-03 21:11:39.599][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 21:11:39.600][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-05-03 21:11:39.602][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:39.603][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:39.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:39.608][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:39.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:39.610][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:39.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:39.611][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:39.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:39.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.615][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:39.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:39.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.623][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:39.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:39.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:39.628][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:39.628][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:39.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:39.633][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:39.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:39.635][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:39.636][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[2024-05-03 21:11:39.637][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:39.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:39.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.641][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:39.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:39.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.644][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:39.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:39.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:39.648][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-03 21:11:39.649][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:39.650][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:39.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:39.655][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:39.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:39.657][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:39.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:39.659][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.662][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.666][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:39.667][private$selectFields]
biodb.TRACE[2024-05-03 21:11:39.668][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 21:11:39.669][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 21:11:39.670][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:39.671][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.671][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.672][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.673][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.674][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.675][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.676][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.677][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.678][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:39.679][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:39.680][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.680][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.681][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.682][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.683][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 21:11:39.684][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.688][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.691][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.704][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-05-03 21:11:39.705][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:39.706][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:39.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:39.710][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:39.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:39.712][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:39.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:39.714][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.718][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.721][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:39.722][private$selectFields]
biodb.TRACE[2024-05-03 21:11:39.723][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 21:11:39.724][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 21:11:39.725][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:39.726][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.727][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.728][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.728][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.729][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.730][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.731][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.732][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.733][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:39.734][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:39.735][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.736][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.737][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.737][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.738][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 21:11:39.739][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.743][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.747][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.751][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-03 21:11:39.752][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:39.753][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:39.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:39.757][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:39.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:39.759][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:39.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:39.761][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.765][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.768][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:39.769][private$selectFields]
biodb.TRACE[2024-05-03 21:11:39.770][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 21:11:39.771][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 21:11:39.772][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:39.773][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.774][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.775][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.780][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.781][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.782][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.783][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.784][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.785][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:39.786][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:39.787][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.788][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.789][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.790][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.791][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 21:11:39.792][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.795][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.799][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:39.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.803][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-05-03 21:11:39.804][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-03 21:11:39.805][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-03 21:11:39.813][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.817][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.821][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:39.824][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:39.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:39.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:39.878][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:39.879][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:39.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:39.884][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:39.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:39.885][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:39.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:39.889][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[2024-05-03 21:11:39.892][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:39.893][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:39.894][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-05-03 21:11:40.352][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-05-03 21:11:40.832][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:40.834][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-05-03 21:11:40.838][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-05-03 21:11:40.841][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-03 21:11:40.844][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:40.845][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:40.847][private$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[2024-05-03 21:11:41.304][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[2024-05-03 21:11:41.766][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:41.768][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-05-03 21:11:41.772][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-05-03 21:11:41.774][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:41.786][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:41.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:41.791][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:41.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:41.793][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:41.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:41.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:41.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:41.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:41.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:41.799][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:41.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:41.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:41.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:41.803][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:41.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:41.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:41.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:41.807][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:41.808][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:41.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:41.814][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:41.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:41.815][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:41.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:41.817][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:41.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:41.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:41.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:41.821][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:41.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:41.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:41.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:41.825][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:41.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:41.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:41.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:41.829][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:41.830][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:41.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:41.835][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:41.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:41.836][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:41.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:41.838][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:41.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:41.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:41.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:41.842][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:41.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:41.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:41.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:41.846][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:41.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:41.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:41.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:41.871][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-03 21:11:41.894][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:41.895][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:41.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:41.900][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:41.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:41.901][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:41.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:41.903][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:41.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:41.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:41.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:41.907][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:41.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:41.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:41.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:41.911][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:41.912][private$selectFields]
biodb.TRACE[2024-05-03 21:11:41.913][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 21:11:41.913][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 21:11:41.914][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:41.915][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:41.916][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:41.917][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:41.918][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:41.919][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:41.920][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:41.921][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:41.922][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:41.923][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:41.924][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:41.924][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:41.925][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:41.926][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:41.927][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:41.928][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 21:11:41.929][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:41.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:41.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:41.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:41.938][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:41.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:41.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:41.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:41.941][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:41.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:41.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:41.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:41.946][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-05-03 21:11:41.947][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:41.947][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:41.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:41.952][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:41.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:41.954][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:41.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:41.967][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:41.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:41.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:41.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:41.971][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:41.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:41.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:41.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:41.993][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:41.994][private$selectFields]
biodb.TRACE[2024-05-03 21:11:41.995][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 21:11:41.996][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 21:11:41.997][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:41.998][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:41.999][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.000][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.001][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.002][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.003][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.004][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.005][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.006][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.015][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.016][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.017][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.018][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.019][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.020][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 21:11:42.021][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.024][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.028][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.032][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-03 21:11:42.033][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:42.034][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:42.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:42.039][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:42.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:42.040][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:42.041][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.TRACE[2024-05-03 21:11:42.042][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.046][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.050][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.051][private$selectFields]
biodb.TRACE[2024-05-03 21:11:42.052][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 21:11:42.053][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 21:11:42.053][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.054][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.055][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.056][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.057][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.058][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.059][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.060][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.061][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.062][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.063][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.064][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.065][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.065][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.066][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.067][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 21:11:42.068][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.072][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.076][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.084][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-05-03 21:11:42.086][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-03 21:11:42.086][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-03 21:11:42.094][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-03 21:11:42.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-03 21:11:42.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-03 21:11:42.100][biodb::testThat]
biodb.INFO [2024-05-03 21:11:42.101][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-05-03 21:11:42.102][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 21:11:42.103][biodb::testThat]
biodb.TRACE[2024-05-03 21:11:42.105][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-03 21:11:42.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-03 21:11:42.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.109][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.113][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.116][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.120][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:42.126][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:42.127][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:42.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:42.131][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:42.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:42.133][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:42.134][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[2024-05-03 21:11:42.136][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[2024-05-03 21:11:42.139][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 21:11:42.140][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-05-03 21:11:42.141][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 21:11:42.143][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-05-03 21:11:42.145][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:42.146][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:42.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:42.150][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:42.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:42.152][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:42.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:42.154][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.158][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.161][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:42.166][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[2024-05-03 21:11:42.169][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 21:11:42.170][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-05-03 21:11:42.171][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 21:11:42.172][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-05-03 21:11:42.175][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:42.176][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:42.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:42.181][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:42.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:42.182][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:42.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:42.184][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.188][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.191][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:42.195][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:42.196][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:42.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:42.201][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:42.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:42.203][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:42.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:42.205][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.208][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.212][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:42.216][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-03 21:11:42.217][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:42.218][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:42.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:42.223][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:42.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:42.225][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:42.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:42.227][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.231][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.234][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.235][private$selectFields]
biodb.TRACE[2024-05-03 21:11:42.236][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 21:11:42.237][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 21:11:42.238][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.239][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.244][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.246][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.247][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.248][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.249][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.250][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.250][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.251][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.252][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.253][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.254][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.255][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.256][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.257][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 21:11:42.258][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.261][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.265][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.269][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-05-03 21:11:42.270][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:42.271][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:42.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:42.276][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:42.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:42.278][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:42.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:42.280][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.283][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.287][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.288][private$selectFields]
biodb.TRACE[2024-05-03 21:11:42.289][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 21:11:42.290][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 21:11:42.290][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.291][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.292][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.293][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.294][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.295][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.296][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.297][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.298][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.299][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.300][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.301][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.301][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.302][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.303][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.304][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 21:11:42.305][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.309][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.313][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.317][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-03 21:11:42.318][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:42.318][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:42.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:42.323][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:42.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:42.325][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:42.326][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[2024-05-03 21:11:42.327][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.331][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.334][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.335][private$selectFields]
biodb.TRACE[2024-05-03 21:11:42.336][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 21:11:42.337][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 21:11:42.338][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.339][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.340][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.341][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.342][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.343][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.343][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.344][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.345][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.346][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.347][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.348][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.349][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.350][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.351][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.352][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 21:11:42.353][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.356][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.360][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.364][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-05-03 21:11:42.365][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-03 21:11:42.366][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-03 21:11:42.373][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:42.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:42.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.377][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:42.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:42.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.381][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:42.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:42.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.385][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:42.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:42.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:42.391][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:42.391][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:42.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:42.396][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:42.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:42.398][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:42.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:42.406][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[2024-05-03 21:11:42.410][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 21:11:42.411][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-05-03 21:11:42.412][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 21:11:42.413][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-05-03 21:11:42.416][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[2024-05-03 21:11:42.419][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 21:11:42.420][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-05-03 21:11:42.421][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 21:11:42.422][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-05-03 21:11:42.425][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:42.425][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:42.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:42.430][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:42.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:42.432][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:42.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:42.434][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:42.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:42.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.438][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:42.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:42.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.442][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:42.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:42.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:42.445][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:42.446][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:42.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:42.451][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:42.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:42.453][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:42.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:42.455][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:42.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:42.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.459][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:42.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:42.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.462][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:42.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:42.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:42.466][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:42.467][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:42.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:42.472][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:42.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:42.474][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:42.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:42.476][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:42.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:42.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.479][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:42.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:42.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.483][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:42.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:42.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:42.487][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-03 21:11:42.488][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:42.489][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:42.490][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:42.494][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:42.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:42.496][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:42.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:42.498][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.502][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.505][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.506][private$selectFields]
biodb.TRACE[2024-05-03 21:11:42.507][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 21:11:42.508][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 21:11:42.509][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.510][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.511][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.512][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.513][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.513][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.514][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.515][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.516][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.517][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.518][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.519][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.520][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.521][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.522][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.523][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 21:11:42.524][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.527][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.531][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.535][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-05-03 21:11:42.536][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:42.537][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:42.538][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:42.542][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:42.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:42.544][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:42.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:42.546][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.549][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.553][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.554][private$selectFields]
biodb.TRACE[2024-05-03 21:11:42.555][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 21:11:42.556][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 21:11:42.557][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.558][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.559][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.559][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.560][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.561][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.567][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.568][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.569][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.570][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.571][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.572][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.573][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.574][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.575][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.576][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 21:11:42.577][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.581][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.584][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.588][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-03 21:11:42.589][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:42.590][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:42.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:42.595][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:42.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:42.597][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:42.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:42.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.603][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.606][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.607][private$selectFields]
biodb.TRACE[2024-05-03 21:11:42.608][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 21:11:42.609][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 21:11:42.610][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.611][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.612][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.613][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.614][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.615][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.616][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.616][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.617][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.618][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.619][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.620][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.621][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.622][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.623][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.624][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 21:11:42.625][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.628][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.632][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.636][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-05-03 21:11:42.637][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-03 21:11:42.638][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-03 21:11:42.645][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-03 21:11:42.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-03 21:11:42.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-03 21:11:42.652][biodb::testThat]
biodb.INFO [2024-05-03 21:11:42.653][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-05-03 21:11:42.654][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 21:11:42.655][biodb::testThat]
biodb.TRACE[2024-05-03 21:11:42.657][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-03 21:11:42.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-03 21:11:42.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.661][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.665][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.669][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.673][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:42.680][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:42.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:42.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:42.686][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:42.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:42.688][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:42.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:42.691][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[2024-05-03 21:11:42.694][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 21:11:42.696][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-05-03 21:11:42.697][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 21:11:42.698][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-05-03 21:11:42.700][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:42.701][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:42.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:42.706][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:42.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:42.708][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:42.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:42.710][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.714][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.718][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:42.722][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[2024-05-03 21:11:42.725][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 21:11:42.732][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-05-03 21:11:42.734][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 21:11:42.735][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-05-03 21:11:42.737][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:42.738][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:42.739][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:42.743][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:42.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:42.745][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:42.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:42.747][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.751][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.754][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:42.758][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:42.759][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:42.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:42.764][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:42.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:42.765][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:42.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:42.767][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.771][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.775][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:42.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:42.778][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-03 21:11:42.780][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:42.781][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:42.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:42.786][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:42.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:42.787][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:42.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:42.789][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.793][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.797][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.797][private$selectFields]
biodb.TRACE[2024-05-03 21:11:42.798][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 21:11:42.799][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 21:11:42.800][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.801][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.802][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.803][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.804][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.805][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.806][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.807][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.807][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.808][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.809][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.810][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.811][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.812][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.813][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.814][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 21:11:42.815][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.818][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.822][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.826][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-05-03 21:11:42.827][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:42.828][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:42.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:42.833][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:42.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:42.835][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:42.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:42.837][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.841][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.844][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.845][private$selectFields]
biodb.TRACE[2024-05-03 21:11:42.846][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 21:11:42.847][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 21:11:42.848][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.849][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.850][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.851][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.851][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.852][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.853][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.855][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.856][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.857][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.858][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.859][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.860][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.861][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.861][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 21:11:42.862][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.866][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.870][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.874][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-03 21:11:42.875][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:42.876][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:42.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:42.881][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:42.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:42.882][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:42.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:42.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.893][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.896][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.897][private$selectFields]
biodb.TRACE[2024-05-03 21:11:42.898][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 21:11:42.899][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 21:11:42.900][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.901][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.902][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.903][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.904][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.905][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.906][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.906][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.907][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.908][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.909][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:42.910][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.911][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.912][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.913][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.914][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 21:11:42.915][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.918][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.926][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:42.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.931][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-05-03 21:11:42.932][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-03 21:11:42.933][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-03 21:11:42.953][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:42.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:42.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.958][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:42.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:42.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.962][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:42.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:42.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:42.966][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:42.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:42.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:42.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:42.975][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:42.976][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:42.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:42.981][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:42.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:42.983][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:42.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:42.987][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[2024-05-03 21:11:42.991][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 21:11:42.992][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-05-03 21:11:42.994][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 21:11:42.995][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-05-03 21:11:42.999][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[2024-05-03 21:11:43.002][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 21:11:43.004][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-05-03 21:11:43.005][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 21:11:43.006][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-05-03 21:11:43.008][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:43.009][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:43.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:43.015][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:43.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:43.017][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:43.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:43.019][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:43.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:43.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:43.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:43.023][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:43.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:43.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:43.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:43.027][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:43.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:43.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:43.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:43.031][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:43.032][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:43.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:43.038][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:43.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:43.040][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:43.041][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.TRACE[2024-05-03 21:11:43.042][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:43.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:43.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:43.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:43.046][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:43.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:43.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:43.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:43.050][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:43.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:43.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:43.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:43.054][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:43.055][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:43.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:43.060][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:43.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:43.062][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:43.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:43.064][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:43.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:43.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:43.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:43.068][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:43.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:43.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:43.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:43.086][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:43.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:43.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:43.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:43.090][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-03 21:11:43.092][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:43.093][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:43.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:43.098][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:43.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:43.100][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:43.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:43.102][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:43.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:43.106][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:43.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:43.110][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:43.111][private$selectFields]
biodb.TRACE[2024-05-03 21:11:43.112][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 21:11:43.113][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 21:11:43.113][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:43.115][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.116][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.116][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:43.117][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:43.118][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.119][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.120][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:43.121][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:43.122][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:43.123][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:43.124][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.125][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.126][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:43.127][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:43.128][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 21:11:43.129][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:43.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:43.133][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:43.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:43.136][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:43.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:43.140][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-05-03 21:11:43.141][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:43.142][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:43.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:43.147][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:43.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:43.149][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:43.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:43.151][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:43.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:43.154][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:43.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:43.158][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:43.159][private$selectFields]
biodb.TRACE[2024-05-03 21:11:43.160][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 21:11:43.161][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 21:11:43.162][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:43.163][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.164][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.164][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:43.165][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:43.166][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.167][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.168][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:43.169][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:43.170][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:43.171][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:43.172][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.173][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.174][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:43.174][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:43.175][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 21:11:43.176][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:43.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:43.180][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:43.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:43.184][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:43.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:43.188][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-03 21:11:43.189][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:43.189][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:43.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:43.194][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:43.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:43.196][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:43.197][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[2024-05-03 21:11:43.198][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:43.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:43.202][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:43.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:43.205][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:43.206][private$selectFields]
biodb.TRACE[2024-05-03 21:11:43.207][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 21:11:43.208][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 21:11:43.209][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:43.210][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.211][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.212][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:43.213][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:43.214][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.215][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.215][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:43.216][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:43.217][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:43.218][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 21:11:43.219][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.220][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.221][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:43.222][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:43.223][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 21:11:43.224][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:43.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:43.227][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:43.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:43.231][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:43.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:43.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:43.235][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-05-03 21:11:43.236][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-03 21:11:43.237][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-03 21:11:43.257][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-03 21:11:43.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-03 21:11:43.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:43.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-03 21:11:43.264][biodb::testThat]
biodb.INFO [2024-05-03 21:11:43.265][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-05-03 21:11:43.266][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 21:11:43.266][biodb::testThat]
biodb.DEBUG[2024-05-03 21:11:43.268][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-05-03 21:11:43.269][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 21:11:43.270][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-05-03 21:11:43.272][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 21:11:43.273][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 21:11:43.274][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 21:11:43.275][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 21:11:43.276][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 21:11:43.276][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 21:11:43.279][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:43.280][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:43.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:43.284][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:43.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:43.286][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:43.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:43.288][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-05-03 21:11:43.291][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:43.291][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:43.293][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-05-03 21:11:43.748][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-05-03 21:11:44.229][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:44.232][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-05-03 21:11:44.237][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-05-03 21:11:44.240][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-05-03 21:11:44.242][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 21:11:44.244][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 21:11:44.246][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 21:11:44.248][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:44.249][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:44.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:44.257][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:44.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:44.260][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:44.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:44.264][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:44.266][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:44.267][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:44.269][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:44.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:44.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:44.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:44.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:44.276][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:44.278][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:44.279][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:44.280][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:44.282][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:44.284][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:44.285][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:44.286][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:44.289][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:44.290][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:44.291][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:44.293][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:44.295][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:44.296][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:44.297][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:44.299][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:44.300][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:44.302][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:44.303][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:44.305][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:44.307][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:44.308][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:44.309][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:44.311][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:44.313][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:44.314][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:44.315][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:44.317][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:44.319][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:44.320][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:44.321][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:44.323][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:44.325][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:44.326][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:44.328][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:44.329][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:44.331][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:44.332][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:44.334][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:44.335][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:44.337][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:44.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:44.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:44.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:44.343][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:44.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:44.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:44.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:44.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:44.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:44.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:44.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:44.354][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:44.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:44.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:44.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:44.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:44.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:44.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:44.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:44.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:44.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:44.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:44.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:44.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:44.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:44.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:44.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:44.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:44.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:44.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:44.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:44.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:44.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:44.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:44.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:44.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:44.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:44.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:44.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:44.400][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-03 21:11:44.401][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-05-03 21:11:44.408][biodb::testThat]
biodb.INFO [2024-05-03 21:11:44.409][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-05-03 21:11:44.410][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 21:11:44.411][biodb::testThat]
biodb.DEBUG[2024-05-03 21:11:44.419][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-05-03 21:11:44.420][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-05-03 21:11:44.421][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-05-03 21:11:44.423][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-05-03 21:11:44.424][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2024-05-03 21:11:44.425][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 21:11:44.426][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 21:11:44.427][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 21:11:44.428][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 21:11:44.429][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 21:11:44.433][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:44.434][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:44.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:44.440][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:44.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:44.441][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:44.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:44.444][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2024-05-03 21:11:44.447][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:44.449][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:44.451][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-05-03 21:11:44.914][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-05-03 21:11:45.407][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:45.409][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-05-03 21:11:45.412][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-05-03 21:11:45.413][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:45.414][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:45.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:45.420][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:45.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:45.421][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:45.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:45.424][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2024-05-03 21:11:45.426][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:45.427][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:45.428][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2024-05-03 21:11:45.931][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2024-05-03 21:11:46.422][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:46.424][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2024-05-03 21:11:46.427][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2024-05-03 21:11:46.428][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:46.429][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:46.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:46.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:46.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:46.436][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:46.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:46.438][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2024-05-03 21:11:46.441][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:46.441][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:46.443][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-05-03 21:11:46.901][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2024-05-03 21:11:47.383][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:47.386][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-05-03 21:11:47.389][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-05-03 21:11:47.391][private$doSaveContentToFile] Saving to cache [3]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2024-05-03 21:11:47.393][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 21:11:47.394][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-05-03 21:11:47.395][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-05-03 21:11:47.397][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:47.397][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:47.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:47.403][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:47.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:47.405][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:47.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:47.408][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:47.409][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:47.410][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.411][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:47.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:47.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.416][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:47.417][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:47.418][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.419][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.420][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:47.421][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:47.422][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.423][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.424][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:47.425][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:47.426][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.427][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.429][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:47.430][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:47.431][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.431][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.433][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:47.434][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:47.435][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.436][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.437][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:47.438][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:47.439][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.439][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.441][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:47.454][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:47.455][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.456][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.458][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:47.459][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:47.460][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.461][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.462][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:47.463][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:47.464][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.465][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.466][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:47.467][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:47.468][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.469][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.470][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:47.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:47.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.473][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:47.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:47.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:47.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:47.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.481][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:47.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:47.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:47.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:47.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:47.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:47.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.492][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:47.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:47.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:47.496][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:47.497][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:47.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:47.502][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:47.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:47.503][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:47.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:47.506][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:47.507][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:47.508][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.509][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:47.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:47.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.514][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:47.515][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:47.516][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.517][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.518][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:47.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:47.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.521][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:47.522][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:47.523][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.524][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.526][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:47.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:47.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.529][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:47.530][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:47.531][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.532][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.533][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:47.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:47.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.537][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:47.538][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:47.539][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.540][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.541][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:47.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:47.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.545][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:47.546][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:47.546][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.547][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.548][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:47.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:47.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.552][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:47.553][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:47.554][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.555][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.556][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:47.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:47.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.560][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:47.561][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:47.562][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.563][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.564][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:47.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:47.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.567][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:47.568][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:47.569][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.570][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.571][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:47.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:47.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.575][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:47.576][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:47.577][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.578][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.579][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:47.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:47.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.583][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:47.584][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:47.585][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.586][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.587][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:47.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:47.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.591][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:47.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:47.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.594][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:47.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:47.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:47.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:47.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.602][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:47.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:47.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:47.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:47.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:47.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:47.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:47.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:47.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:47.622][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:47.623][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:47.624][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:47.628][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:47.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:47.629][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:47.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 21:11:47.633][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:47.634][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:47.635][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.636][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:47.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:47.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.640][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:47.641][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:47.642][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.643][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.644][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:47.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:47.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.648][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:47.649][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:47.650][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.651][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.652][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:47.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:47.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.656][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:47.657][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:47.658][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.659][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.660][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:47.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:47.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.663][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:47.664][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:47.665][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.666][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.667][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:47.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:47.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.671][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:47.672][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:47.673][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.674][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.675][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:47.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:47.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.678][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:47.679][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:47.680][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.681][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.682][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:47.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:47.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.686][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:47.687][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:47.688][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.689][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.690][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:47.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:47.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.694][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:47.695][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:47.696][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.696][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.698][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:47.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:47.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.701][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:47.702][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:47.703][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.704][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.705][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:47.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:47.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.709][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:47.710][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:47.711][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.712][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.713][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:47.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:47.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.717][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:47.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:47.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.720][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:47.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:47.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:47.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:47.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.728][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:47.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:47.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.732][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:47.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:47.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:47.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:47.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:47.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:47.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:47.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:47.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:47.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:47.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:47.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:47.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:47.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:47.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:47.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:47.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:47.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:47.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:47.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:47.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:47.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:47.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:47.777][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:47.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:47.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:47.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:47.781][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-05-03 21:11:47.782][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-03 21:11:47.783][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-05-03 21:11:47.793][biodb::testThat]
biodb.INFO [2024-05-03 21:11:47.794][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-05-03 21:11:47.795][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 21:11:47.796][biodb::testThat]
biodb.INFO [2024-05-03 21:11:47.817][biodb::testThat]
biodb.INFO [2024-05-03 21:11:47.818][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-05-03 21:11:47.819][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 21:11:47.819][biodb::testThat]
biodb.INFO [2024-05-03 21:11:47.826][biodb::testThat]
biodb.INFO [2024-05-03 21:11:47.827][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-05-03 21:11:47.828][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 21:11:47.829][biodb::testThat]
biodb.DEBUG[2024-05-03 21:11:47.831][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[2024-05-03 21:11:47.834][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:47.835][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:47.836][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2024-05-03 21:11:48.359][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2024-05-03 21:11:48.982][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:48.985][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-05-03 21:11:48.988][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-05-03 21:11:48.998][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:48.999][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:49.000][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:49.001][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:49.002][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:49.003][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:49.004][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:49.005][ef$get] fields variable is a list.
biodb.INFO [2024-05-03 21:11:49.006][biodb::testThat]
biodb.INFO [2024-05-03 21:11:49.007][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-05-03 21:11:49.008][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 21:11:49.009][biodb::testThat]
biodb.ERROR[2024-05-03 21:11:49.021][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-05-03 21:11:49.037][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-05-03 21:11:49.050][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-03 21:11:49.051][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-05-03 21:11:49.052][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-05-03 21:11:49.053][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-03 21:11:49.054][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:49.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:49.055][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.057][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-03 21:11:49.076][biodb::testContext]
biodb.INFO [2024-05-03 21:11:49.077][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-03 21:11:49.078][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-05-03 21:11:49.079][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-03 21:11:49.080][biodb::testContext]
biodb.INFO [2024-05-03 21:11:49.082][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-03 21:11:49.083][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-05-03 21:11:49.087][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-03 21:11:49.088][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-03 21:11:49.089][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-03 21:11:49.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.092][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-03 21:11:49.093][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-03 21:11:49.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.097][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-03 21:11:49.098][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-03 21:11:49.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.101][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-03 21:11:49.102][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-03 21:11:49.103][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-03 21:11:49.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.106][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-03 21:11:49.107][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-03 21:11:49.108][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-03 21:11:49.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.111][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[2024-05-03 21:11:49.111][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-03 21:11:49.112][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-03 21:11:49.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.116][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-03 21:11:49.117][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-03 21:11:49.118][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-03 21:11:49.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.121][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-03 21:11:49.122][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-03 21:11:49.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.125][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-03 21:11:49.126][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-03 21:11:49.127][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-03 21:11:49.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.130][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-03 21:11:49.131][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-03 21:11:49.132][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-03 21:11:49.133][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-03 21:11:49.134][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-03 21:11:49.135][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-03 21:11:49.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.138][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-03 21:11:49.139][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-03 21:11:49.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.143][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-03 21:11:49.144][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-03 21:11:49.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.147][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-03 21:11:49.148][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-03 21:11:49.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.151][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-03 21:11:49.152][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-03 21:11:49.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.156][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-03 21:11:49.157][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-03 21:11:49.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.159][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[2024-05-03 21:11:49.160][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-03 21:11:49.161][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-03 21:11:49.164][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-03 21:11:49.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.167][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-03 21:11:49.168][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-03 21:11:49.169][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-03 21:11:49.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.171][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[2024-05-03 21:11:49.173][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-03 21:11:49.174][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:49.175][self$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[2024-05-03 21:11:49.176][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:49.177][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 21:11:49.178][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:49.179][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 21:11:49.180][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:49.181][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 21:11:49.182][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-03 21:11:49.183][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 21:11:49.183][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:49.184][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-03 21:11:49.185][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 21:11:49.186][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:49.187][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:49.188][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-03 21:11:49.188][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-03 21:11:49.188][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-03 21:11:49.188][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-03 21:11:49.188][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-03 21:11:49.189][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 21:11:49.190][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:11:49.191][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:11:49.192][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 21:11:49.193][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:11:49.193][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:11:49.194][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 21:11:49.195][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:49.196][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 21:11:49.197][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 21:11:49.198][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:49.199][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:49.200][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-03 21:11:49.202][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:49.202][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-03 21:11:49.203][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:49.204][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 21:11:49.205][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:49.206][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 21:11:49.207][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:49.208][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 21:11:49.209][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-03 21:11:49.210][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 21:11:49.211][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:49.212][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-03 21:11:49.213][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 21:11:49.214][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:49.214][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:49.215][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-03 21:11:49.215][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-03 21:11:49.215][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-03 21:11:49.215][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-03 21:11:49.215][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-03 21:11:49.216][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 21:11:49.217][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:11:49.218][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:11:49.219][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 21:11:49.220][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:11:49.221][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:11:49.389][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 21:11:49.391][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:49.392][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 21:11:49.393][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 21:11:49.394][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:49.395][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:49.396][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-03 21:11:49.397][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:49.398][self$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[2024-05-03 21:11:49.399][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:49.400][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 21:11:49.401][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:49.402][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 21:11:49.403][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:49.403][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 21:11:49.404][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-03 21:11:49.405][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 21:11:49.406][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:49.407][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-03 21:11:49.408][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 21:11:49.409][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:49.410][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:49.411][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:49.411][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 21:11:49.412][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:11:49.413][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:11:49.414][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 21:11:49.415][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:11:49.416][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:11:49.416][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 21:11:49.417][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:49.418][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 21:11:49.419][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 21:11:49.420][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:49.421][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:49.422][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-03 21:11:49.423][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:49.424][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-03 21:11:49.425][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:49.426][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 21:11:49.427][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:49.428][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 21:11:49.429][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:49.430][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 21:11:49.431][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-03 21:11:49.431][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 21:11:49.432][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:49.433][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-03 21:11:49.434][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 21:11:49.435][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:49.436][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:49.437][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:49.438][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 21:11:49.439][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:11:49.439][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:11:49.440][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 21:11:49.441][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:11:49.442][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:11:49.443][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 21:11:49.444][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:49.444][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 21:11:49.445][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 21:11:49.446][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:49.447][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:49.448][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-03 21:11:49.449][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.450][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[2024-05-03 21:11:49.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.470][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[2024-05-03 21:11:49.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.474][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[2024-05-03 21:11:49.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.482][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[2024-05-03 21:11:49.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.486][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[2024-05-03 21:11:49.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.494][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[2024-05-03 21:11:49.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.510][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[2024-05-03 21:11:49.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.519][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-03 21:11:49.520][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-03 21:11:49.522][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-03 21:11:49.523][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-03 21:11:49.524][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-03 21:11:49.526][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-03 21:11:49.527][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-03 21:11:49.528][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-03 21:11:49.529][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-03 21:11:49.531][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-03 21:11:49.532][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-03 21:11:49.533][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-03 21:11:49.534][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-03 21:11:49.536][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-03 21:11:49.537][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-03 21:11:49.538][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-03 21:11:49.540][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-03 21:11:49.541][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-03 21:11:49.542][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-03 21:11:49.543][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-03 21:11:49.545][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-03 21:11:49.546][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-03 21:11:49.547][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-03 21:11:49.549][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-03 21:11:49.550][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-03 21:11:49.551][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-03 21:11:49.553][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-03 21:11:49.554][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-03 21:11:49.556][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-03 21:11:49.557][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-03 21:11:49.558][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-03 21:11:49.560][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-03 21:11:49.561][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-03 21:11:49.563][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-03 21:11:49.564][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-03 21:11:49.565][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-03 21:11:49.567][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-03 21:11:49.568][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-03 21:11:49.570][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-03 21:11:49.571][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-03 21:11:49.573][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-03 21:11:49.574][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-03 21:11:49.575][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-03 21:11:49.577][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-03 21:11:49.578][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-03 21:11:49.580][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-03 21:11:49.581][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-03 21:11:49.583][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-03 21:11:49.584][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-03 21:11:49.586][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-03 21:11:49.587][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-03 21:11:49.589][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-03 21:11:49.590][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-03 21:11:49.591][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-03 21:11:49.593][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-03 21:11:49.594][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-03 21:11:49.596][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-03 21:11:49.597][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-03 21:11:49.599][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-03 21:11:49.600][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-03 21:11:49.602][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-03 21:11:49.603][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-03 21:11:49.604][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-03 21:11:49.606][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-03 21:11:49.607][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-03 21:11:49.609][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-03 21:11:49.610][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-03 21:11:49.612][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-03 21:11:49.613][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-03 21:11:49.614][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-03 21:11:49.616][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-03 21:11:49.617][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-03 21:11:49.619][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-03 21:11:49.620][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-03 21:11:49.622][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-03 21:11:49.623][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-03 21:11:49.624][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-03 21:11:49.626][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-03 21:11:49.627][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-03 21:11:49.629][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-03 21:11:49.630][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-03 21:11:49.632][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-03 21:11:49.633][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-03 21:11:49.635][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-03 21:11:49.636][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-03 21:11:49.637][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-03 21:11:49.638][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.640][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.641][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[2024-05-03 21:11:49.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:49.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:49.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:49.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:49.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:49.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:49.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:49.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:49.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:49.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:49.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:49.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:49.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:49.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:49.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:49.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:49.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:49.698][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:49.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:49.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:49.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:49.709][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:49.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:49.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:49.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:49.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:49.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:49.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:49.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:49.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:49.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:49.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:49.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:49.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:49.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:49.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:49.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:49.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:49.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:49.747][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-05-03 21:11:49.748][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-05-03 21:11:49.750][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:49.751][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-03 21:11:49.752][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:49.753][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 21:11:49.754][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:49.755][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 21:11:49.755][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:49.756][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-05-03 21:11:49.757][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-03 21:11:49.758][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 21:11:49.759][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:49.760][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-05-03 21:11:49.761][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 21:11:49.762][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-05-03 21:11:49.762][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-05-03 21:11:49.762][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-05-03 21:11:49.762][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-05-03 21:11:49.762][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-05-03 21:11:49.762][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-05-03 21:11:49.762][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-05-03 21:11:49.762][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-05-03 21:11:49.762][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-05-03 21:11:49.762][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-05-03 21:11:49.762][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-05-03 21:11:49.763][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:49.764][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-03 21:11:49.764][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-03 21:11:49.764][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-03 21:11:49.765][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-03 21:11:49.766][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:11:49.766][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:11:49.767][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 21:11:49.768][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:11:49.769][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:11:49.770][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 21:11:49.771][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 21:11:49.771][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-05-03 21:11:49.772][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 21:11:49.772][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 21:11:49.773][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:49.774][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-05-03 21:11:49.774][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-05-03 21:11:49.775][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-03 21:11:49.777][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-03 21:11:49.778][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-05-03 21:11:49.779][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-03 21:11:49.781][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-03 21:11:49.782][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-03 21:11:49.785][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-05-03 21:11:49.786][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-05-03 21:11:49.787][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-05-03 21:11:49.789][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-05-03 21:11:49.790][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-03 21:11:49.791][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-03 21:11:49.792][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-05-03 21:11:49.793][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-05-03 21:11:49.794][biodb::testThat]
biodb.INFO [2024-05-03 21:11:49.795][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2024-05-03 21:11:49.796][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 21:11:49.797][biodb::testThat]
biodb.DEBUG[2024-05-03 21:11:49.800][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-05-03 21:11:49.803][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 21:11:49.805][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-05-03 21:11:49.806][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 21:11:49.807][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-05-03 21:11:49.810][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-03 21:11:49.813][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:49.814][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:49.816][private$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[2024-05-03 21:11:50.276][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[2024-05-03 21:11:50.737][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:50.739][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2024-05-03 21:11:50.743][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2024-05-03 21:11:50.745][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:50.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:50.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:50.751][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:50.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:50.753][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:50.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:50.755][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[2024-05-03 21:11:50.759][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:50.759][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:50.761][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-05-03 21:11:51.223][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-05-03 21:11:51.997][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:51.999][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2024-05-03 21:11:52.004][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2024-05-03 21:11:52.006][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:52.008][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:52.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:52.014][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:52.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:52.016][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:52.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:52.038][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:52.039][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:52.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:52.045][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:52.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:52.048][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:52.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:52.054][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-03 21:11:52.057][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 21:11:52.059][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-05-03 21:11:52.060][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 21:11:52.061][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-05-03 21:11:52.063][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:52.064][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:52.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:52.069][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:52.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:52.070][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:52.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:52.073][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-03 21:11:52.076][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 21:11:52.077][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-05-03 21:11:52.078][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 21:11:52.079][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-05-03 21:11:52.081][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:52.082][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:52.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:52.087][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:52.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:52.088][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:52.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:52.090][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:52.091][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:52.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:52.096][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:52.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:52.098][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:52.098][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[2024-05-03 21:11:52.102][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-03 21:11:52.105][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 21:11:52.106][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-05-03 21:11:52.107][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 21:11:52.108][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-05-03 21:11:52.110][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:52.111][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:52.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:52.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:52.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:52.118][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:52.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:52.120][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-03 21:11:52.123][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 21:11:52.124][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-05-03 21:11:52.125][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 21:11:52.127][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-05-03 21:11:52.128][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:52.129][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:52.130][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:52.144][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:52.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:52.146][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:52.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:52.148][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-03 21:11:52.151][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:52.152][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:52.154][private$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[2024-05-03 21:11:52.615][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[2024-05-03 21:11:53.117][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:53.119][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2024-05-03 21:11:53.123][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2024-05-03 21:11:53.125][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:53.125][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:53.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:53.130][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:53.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:53.132][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:53.133][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.INFO [2024-05-03 21:11:53.138][biodb::testThat]
biodb.INFO [2024-05-03 21:11:53.139][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2024-05-03 21:11:53.140][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 21:11:53.141][biodb::testThat]
biodb.DEBUG[2024-05-03 21:11:53.144][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[2024-05-03 21:11:53.147][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:53.148][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:53.150][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-05-03 21:11:53.612][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-05-03 21:11:54.074][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:54.076][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-05-03 21:11:54.080][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-05-03 21:11:54.082][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:54.083][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:54.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:54.088][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:54.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:54.090][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:54.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:54.094][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-03 21:11:54.097][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:54.098][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:54.100][private$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[2024-05-03 21:11:54.558][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[2024-05-03 21:11:55.064][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:55.066][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-05-03 21:11:55.069][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-05-03 21:11:55.071][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:55.072][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:55.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:55.077][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.079][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-03 21:11:55.084][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-03 21:11:55.086][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-05-03 21:11:55.087][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-05-03 21:11:55.087][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-03 21:11:55.088][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:55.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:55.090][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.092][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.093][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.INFO [2024-05-03 21:11:55.096][biodb::testContext]
biodb.INFO [2024-05-03 21:11:55.097][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-03 21:11:55.098][biodb::testContext] Test context - Test web services
biodb.INFO [2024-05-03 21:11:55.099][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-03 21:11:55.100][biodb::testContext]
biodb.INFO [2024-05-03 21:11:55.102][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-03 21:11:55.103][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-05-03 21:11:55.107][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-03 21:11:55.108][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-03 21:11:55.109][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-03 21:11:55.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.113][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-03 21:11:55.114][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-03 21:11:55.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.117][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[2024-05-03 21:11:55.117][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-03 21:11:55.119][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-03 21:11:55.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.122][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-03 21:11:55.123][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-03 21:11:55.124][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-03 21:11:55.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.127][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-03 21:11:55.128][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-03 21:11:55.129][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-03 21:11:55.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.133][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-03 21:11:55.134][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-03 21:11:55.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.137][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-03 21:11:55.138][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-03 21:11:55.139][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-03 21:11:55.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.142][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-03 21:11:55.143][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-03 21:11:55.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.146][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-03 21:11:55.147][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-03 21:11:55.148][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-03 21:11:55.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.152][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-03 21:11:55.153][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-03 21:11:55.153][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-03 21:11:55.154][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-03 21:11:55.155][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-03 21:11:55.156][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-03 21:11:55.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.159][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[2024-05-03 21:11:55.160][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-03 21:11:55.160][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-03 21:11:55.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.164][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-03 21:11:55.165][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-03 21:11:55.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.167][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[2024-05-03 21:11:55.168][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-03 21:11:55.169][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-03 21:11:55.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.172][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-03 21:11:55.173][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-03 21:11:55.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.176][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[2024-05-03 21:11:55.177][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-03 21:11:55.178][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-03 21:11:55.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.181][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-03 21:11:55.182][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-03 21:11:55.185][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-03 21:11:55.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.187][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[2024-05-03 21:11:55.188][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-03 21:11:55.189][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-03 21:11:55.190][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-03 21:11:55.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.193][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-03 21:11:55.195][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:55.196][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-03 21:11:55.197][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:55.198][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 21:11:55.199][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:55.200][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 21:11:55.201][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:55.201][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 21:11:55.202][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-03 21:11:55.203][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 21:11:55.204][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:55.205][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-03 21:11:55.206][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 21:11:55.207][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:55.208][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:55.209][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-03 21:11:55.209][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-03 21:11:55.209][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-03 21:11:55.209][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-03 21:11:55.209][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-03 21:11:55.210][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 21:11:55.211][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:11:55.211][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:11:55.212][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 21:11:55.213][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:11:55.214][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:11:55.215][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 21:11:55.216][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:55.217][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 21:11:55.218][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 21:11:55.219][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:55.220][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:55.221][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-03 21:11:55.222][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:55.223][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-03 21:11:55.224][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:55.225][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 21:11:55.226][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:55.227][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 21:11:55.228][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:55.229][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 21:11:55.230][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-03 21:11:55.231][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 21:11:55.232][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:55.232][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-03 21:11:55.233][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 21:11:55.234][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:55.235][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:55.236][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-03 21:11:55.236][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-03 21:11:55.236][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-03 21:11:55.236][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-03 21:11:55.236][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-03 21:11:55.237][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 21:11:55.238][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:11:55.239][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:11:55.240][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 21:11:55.241][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:11:55.241][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:11:55.242][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 21:11:55.243][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:55.244][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 21:11:55.245][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 21:11:55.246][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:55.247][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:55.248][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-03 21:11:55.249][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:55.250][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-03 21:11:55.251][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:55.252][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 21:11:55.253][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:55.254][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 21:11:55.255][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:55.256][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 21:11:55.257][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-03 21:11:55.258][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 21:11:55.259][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:55.259][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-03 21:11:55.260][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 21:11:55.261][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:55.262][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:55.263][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:55.264][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 21:11:55.265][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:11:55.266][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:11:55.267][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 21:11:55.267][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:11:55.268][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:11:55.269][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 21:11:55.270][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:55.271][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 21:11:55.272][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 21:11:55.273][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:55.274][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:55.287][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-03 21:11:55.289][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:55.290][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-03 21:11:55.290][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:55.291][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 21:11:55.292][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:55.293][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 21:11:55.294][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:55.295][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 21:11:55.296][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-03 21:11:55.297][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 21:11:55.298][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:55.298][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-03 21:11:55.299][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 21:11:55.300][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:55.301][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:55.302][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:55.303][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 21:11:55.304][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:11:55.305][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:11:55.305][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 21:11:55.306][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:11:55.307][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:11:55.308][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 21:11:55.309][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:55.310][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 21:11:55.311][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 21:11:55.311][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:55.312][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:55.313][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-03 21:11:55.314][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.319][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[2024-05-03 21:11:55.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.335][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.DEBUG[2024-05-03 21:11:55.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.347][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[2024-05-03 21:11:55.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.356][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.368][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.384][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-03 21:11:55.385][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-03 21:11:55.386][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-03 21:11:55.388][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-03 21:11:55.389][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-03 21:11:55.390][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-03 21:11:55.391][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-03 21:11:55.393][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-03 21:11:55.394][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-03 21:11:55.395][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-03 21:11:55.396][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-03 21:11:55.398][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-03 21:11:55.399][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-03 21:11:55.400][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-03 21:11:55.402][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-03 21:11:55.403][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-03 21:11:55.404][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-03 21:11:55.405][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-03 21:11:55.407][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-03 21:11:55.408][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-03 21:11:55.409][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-03 21:11:55.411][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-03 21:11:55.412][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-03 21:11:55.413][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-03 21:11:55.415][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-03 21:11:55.416][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-03 21:11:55.417][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-03 21:11:55.418][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-03 21:11:55.420][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-03 21:11:55.421][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-03 21:11:55.422][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-03 21:11:55.424][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-03 21:11:55.425][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-03 21:11:55.426][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-03 21:11:55.427][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-03 21:11:55.429][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-03 21:11:55.430][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-03 21:11:55.431][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-03 21:11:55.432][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-03 21:11:55.434][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-03 21:11:55.435][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-03 21:11:55.436][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-03 21:11:55.438][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-03 21:11:55.439][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-03 21:11:55.440][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-03 21:11:55.442][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-03 21:11:55.443][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-03 21:11:55.444][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-03 21:11:55.445][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-03 21:11:55.447][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-03 21:11:55.448][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-03 21:11:55.449][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-03 21:11:55.450][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-03 21:11:55.452][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-03 21:11:55.453][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-03 21:11:55.454][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-03 21:11:55.456][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-03 21:11:55.457][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-03 21:11:55.458][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-03 21:11:55.459][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-03 21:11:55.461][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-03 21:11:55.462][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-03 21:11:55.463][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-03 21:11:55.464][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-03 21:11:55.466][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-03 21:11:55.467][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-03 21:11:55.468][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-03 21:11:55.470][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-03 21:11:55.471][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-03 21:11:55.472][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-03 21:11:55.474][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-03 21:11:55.475][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-03 21:11:55.476][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-03 21:11:55.477][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-03 21:11:55.479][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-03 21:11:55.480][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-03 21:11:55.481][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-03 21:11:55.483][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-03 21:11:55.484][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-03 21:11:55.485][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-03 21:11:55.486][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-03 21:11:55.488][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-03 21:11:55.489][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-03 21:11:55.490][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-03 21:11:55.492][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-03 21:11:55.493][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-03 21:11:55.494][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.495][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:55.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:55.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:55.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:55.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:55.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:55.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:55.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:55.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:55.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:55.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.525][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[2024-05-03 21:11:55.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:55.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:55.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:55.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:55.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:55.538][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:55.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:55.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:55.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:55.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:55.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.553][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.DEBUG[2024-05-03 21:11:55.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:55.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:55.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.563][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[2024-05-03 21:11:55.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:55.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:55.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.569][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[2024-05-03 21:11:55.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:55.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:55.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.574][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[2024-05-03 21:11:55.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:55.577][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:55.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:55.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:55.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.585][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[2024-05-03 21:11:55.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:55.588][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:55.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.591][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[2024-05-03 21:11:55.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:55.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:55.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:55.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:55.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:55.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:55.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:55.598][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-05-03 21:11:55.599][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-05-03 21:11:55.601][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:55.602][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-03 21:11:55.603][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:55.604][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 21:11:55.604][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:55.605][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 21:11:55.606][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:55.607][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-05-03 21:11:55.608][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-03 21:11:55.609][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 21:11:55.610][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:55.611][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-05-03 21:11:55.612][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 21:11:55.612][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-05-03 21:11:55.612][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-05-03 21:11:55.612][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-05-03 21:11:55.612][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-05-03 21:11:55.612][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-05-03 21:11:55.612][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-05-03 21:11:55.612][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-05-03 21:11:55.612][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-05-03 21:11:55.612][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-05-03 21:11:55.612][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-05-03 21:11:55.612][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-05-03 21:11:55.614][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:55.614][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-03 21:11:55.614][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-03 21:11:55.614][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-03 21:11:55.615][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-03 21:11:55.616][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:11:55.617][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:11:55.618][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 21:11:55.619][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:11:55.620][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:11:55.621][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 21:11:55.621][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 21:11:55.621][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-05-03 21:11:55.622][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 21:11:55.623][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 21:11:55.624][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:55.625][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-05-03 21:11:55.625][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-05-03 21:11:55.626][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-03 21:11:55.627][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-03 21:11:55.629][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-05-03 21:11:55.630][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-03 21:11:55.631][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-03 21:11:55.633][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-03 21:11:55.636][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-05-03 21:11:55.637][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-05-03 21:11:55.638][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-05-03 21:11:55.639][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-05-03 21:11:55.640][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-03 21:11:55.641][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-03 21:11:55.642][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-05-03 21:11:55.643][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-05-03 21:11:55.644][biodb::testThat]
biodb.INFO [2024-05-03 21:11:55.645][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-05-03 21:11:55.646][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 21:11:55.647][biodb::testThat]
biodb.DEBUG[2024-05-03 21:11:55.650][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-05-03 21:11:55.653][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 21:11:55.654][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-05-03 21:11:55.655][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 21:11:55.656][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-05-03 21:11:55.659][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[2024-05-03 21:11:55.662][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:55.663][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:55.665][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-05-03 21:11:56.123][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-05-03 21:11:56.605][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:56.608][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-05-03 21:11:56.612][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-05-03 21:11:56.620][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-03 21:11:56.621][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-05-03 21:11:56.622][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-05-03 21:11:56.623][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-03 21:11:56.624][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:56.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:56.626][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:56.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:56.627][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-03 21:11:56.632][biodb::testContext]
biodb.INFO [2024-05-03 21:11:56.633][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-03 21:11:56.634][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-05-03 21:11:56.634][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-03 21:11:56.635][biodb::testContext]
biodb.INFO [2024-05-03 21:11:56.637][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-03 21:11:56.639][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-05-03 21:11:56.643][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-03 21:11:56.644][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-03 21:11:56.645][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-03 21:11:56.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:56.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:56.648][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-03 21:11:56.649][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-03 21:11:56.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:56.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:56.653][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-03 21:11:56.654][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-03 21:11:56.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:56.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:56.657][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-03 21:11:56.658][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-03 21:11:56.659][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-03 21:11:56.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:56.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:56.663][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-03 21:11:56.664][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-03 21:11:56.665][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-03 21:11:56.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:56.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:56.668][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-03 21:11:56.669][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-03 21:11:56.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:56.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:56.672][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-03 21:11:56.673][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-03 21:11:56.674][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-03 21:11:56.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:56.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:56.677][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-03 21:11:56.678][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-03 21:11:56.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:56.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:56.682][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-03 21:11:56.682][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-03 21:11:56.683][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-03 21:11:56.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:56.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:56.687][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-03 21:11:56.688][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-03 21:11:56.689][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-03 21:11:56.690][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-03 21:11:56.690][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-03 21:11:56.691][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-03 21:11:56.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:56.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:56.695][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-03 21:11:56.696][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-03 21:11:56.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:56.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:56.699][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-03 21:11:56.700][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-03 21:11:56.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:56.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:56.703][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-03 21:11:56.704][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-03 21:11:56.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:56.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:56.708][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-03 21:11:56.709][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-03 21:11:56.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:56.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:56.712][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-03 21:11:56.713][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-03 21:11:56.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:56.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:56.716][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-03 21:11:56.717][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-03 21:11:56.720][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-03 21:11:56.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:56.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:56.724][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-03 21:11:56.724][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-03 21:11:56.725][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-03 21:11:56.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:56.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:56.729][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-03 21:11:56.731][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:56.732][self$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[2024-05-03 21:11:56.732][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:56.733][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 21:11:56.734][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:56.735][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 21:11:56.736][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:56.737][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 21:11:56.738][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-03 21:11:56.739][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 21:11:56.740][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:56.741][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-03 21:11:56.742][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 21:11:56.743][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:56.743][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:56.744][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-03 21:11:56.744][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-03 21:11:56.744][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-03 21:11:56.744][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-03 21:11:56.744][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-03 21:11:56.745][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 21:11:56.746][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:11:56.747][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:11:56.748][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 21:11:56.749][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:11:56.750][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:11:56.750][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 21:11:56.751][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:56.752][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 21:11:56.753][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 21:11:56.754][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:56.755][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:56.756][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-03 21:11:56.758][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:56.759][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-03 21:11:56.759][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:56.760][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 21:11:56.761][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:56.762][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 21:11:56.763][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:56.764][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 21:11:56.765][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-03 21:11:56.766][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 21:11:56.767][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:56.768][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-03 21:11:56.769][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 21:11:56.770][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:56.771][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:56.771][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-03 21:11:56.771][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-03 21:11:56.771][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-03 21:11:56.771][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-03 21:11:56.771][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-03 21:11:56.772][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 21:11:56.773][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:11:56.774][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:11:56.775][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 21:11:56.776][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:11:56.777][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:11:56.778][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 21:11:56.778][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:56.779][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 21:11:56.780][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 21:11:56.781][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:56.790][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:56.791][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-03 21:11:56.792][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:56.793][self$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[2024-05-03 21:11:56.794][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:56.795][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 21:11:56.796][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:56.797][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 21:11:56.798][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:56.799][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 21:11:56.799][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-03 21:11:56.800][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 21:11:56.801][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:56.802][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-03 21:11:56.803][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 21:11:56.804][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:56.805][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:56.806][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:56.807][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 21:11:56.808][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:11:56.808][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:11:56.809][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 21:11:56.810][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:11:56.811][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:11:56.812][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 21:11:56.813][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:56.814][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 21:11:56.814][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 21:11:56.815][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:56.816][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:56.817][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-03 21:11:56.819][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:56.820][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-03 21:11:56.821][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:56.822][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 21:11:56.822][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:56.823][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 21:11:56.824][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:56.825][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 21:11:56.826][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-03 21:11:56.827][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 21:11:56.828][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:56.829][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-03 21:11:56.830][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 21:11:56.831][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:56.831][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:56.832][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:56.833][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 21:11:56.834][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:11:56.835][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:11:56.836][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 21:11:56.837][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:11:56.837][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:11:56.838][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 21:11:56.839][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:56.840][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 21:11:56.841][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 21:11:56.842][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:56.843][self$setPropertyValue]
biodb.DEBUG[2024-05-03 21:11:56.844][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-03 21:11:56.845][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:56.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:56.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:56.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:56.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:56.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:56.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:56.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:56.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:56.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:56.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:56.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:56.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.858][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[2024-05-03 21:11:56.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:56.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:56.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:56.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.862][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[2024-05-03 21:11:56.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:56.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:56.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:56.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.866][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[2024-05-03 21:11:56.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:56.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:56.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:56.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:56.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:56.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:56.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:56.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:56.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:56.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:56.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:56.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:56.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:56.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:56.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:56.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.882][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[2024-05-03 21:11:56.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:56.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:56.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:56.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.886][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[2024-05-03 21:11:56.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:56.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:56.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:56.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:56.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:56.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:56.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:56.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:56.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:56.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:56.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:56.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:56.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:56.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:56.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:56.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:56.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:56.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:56.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:56.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:56.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:56.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:56.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:56.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:56.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:56.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:56.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:56.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:56.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:56.916][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-03 21:11:56.917][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-03 21:11:56.918][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-03 21:11:56.920][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-03 21:11:56.921][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-03 21:11:56.922][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-03 21:11:56.924][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-03 21:11:56.925][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-03 21:11:56.926][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-03 21:11:56.927][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-03 21:11:56.929][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-03 21:11:56.930][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-03 21:11:56.931][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-03 21:11:56.933][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-03 21:11:56.934][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-03 21:11:56.935][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-03 21:11:56.936][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-03 21:11:56.938][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-03 21:11:56.939][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-03 21:11:56.940][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-03 21:11:56.942][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-03 21:11:56.943][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-03 21:11:56.944][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-03 21:11:56.945][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-03 21:11:56.947][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-03 21:11:56.948][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-03 21:11:56.949][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-03 21:11:56.950][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-03 21:11:56.952][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-03 21:11:56.953][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-03 21:11:56.954][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-03 21:11:56.956][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-03 21:11:56.957][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-03 21:11:56.958][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-03 21:11:56.959][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-03 21:11:56.961][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-03 21:11:56.962][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-03 21:11:56.963][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-03 21:11:56.964][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-03 21:11:56.966][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-03 21:11:56.967][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-03 21:11:56.968][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-03 21:11:56.969][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-03 21:11:56.971][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-03 21:11:56.972][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-03 21:11:56.973][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-03 21:11:56.975][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-03 21:11:56.976][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-03 21:11:56.977][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-03 21:11:56.978][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-03 21:11:56.980][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-03 21:11:56.981][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-03 21:11:56.982][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-03 21:11:56.983][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-03 21:11:56.985][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-03 21:11:56.986][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-03 21:11:56.987][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-03 21:11:56.989][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-03 21:11:56.990][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-03 21:11:56.991][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-03 21:11:56.992][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-03 21:11:56.994][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-03 21:11:56.995][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-03 21:11:56.996][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-03 21:11:56.998][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-03 21:11:56.999][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-03 21:11:57.000][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-03 21:11:57.001][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-03 21:11:57.003][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-03 21:11:57.004][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-03 21:11:57.005][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-03 21:11:57.006][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-03 21:11:57.008][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-03 21:11:57.009][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-03 21:11:57.010][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-03 21:11:57.011][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-03 21:11:57.013][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-03 21:11:57.014][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-03 21:11:57.015][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-03 21:11:57.017][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-03 21:11:57.018][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-03 21:11:57.019][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-03 21:11:57.020][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-03 21:11:57.022][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-03 21:11:57.023][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-03 21:11:57.024][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-03 21:11:57.025][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:57.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:57.027][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:57.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:57.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:57.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:57.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:57.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:57.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:57.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:57.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:57.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:57.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:57.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:57.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:57.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:57.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:57.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:57.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:57.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:57.041][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:57.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:57.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:57.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:57.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:57.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:57.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:57.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:57.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:57.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:57.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:57.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:57.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:57.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:57.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:57.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:57.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:57.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:57.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:57.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:57.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:57.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:57.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:57.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:57.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:57.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:57.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:57.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:57.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:57.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:57.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:57.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:57.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:57.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:57.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:57.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:57.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:57.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:57.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:57.078][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.DEBUG[2024-05-03 21:11:57.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:57.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:57.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:57.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:57.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:57.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:57.084][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[2024-05-03 21:11:57.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:57.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:57.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:57.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:57.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:57.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:57.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:57.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:57.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:57.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:57.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:57.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:57.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:57.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:57.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:57.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:57.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:57.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:57.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:57.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:57.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:57.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:57.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:57.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:57.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:57.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:57.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:57.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:57.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:57.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:57.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:57.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:57.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:57.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:57.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:57.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:57.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:57.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:57.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:57.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:57.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:57.123][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[2024-05-03 21:11:57.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:57.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:57.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:57.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:57.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:57.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:57.129][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[2024-05-03 21:11:57.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 21:11:57.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:57.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:57.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:57.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:57.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:57.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:57.138][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-05-03 21:11:57.140][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-05-03 21:11:57.142][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:57.143][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-03 21:11:57.144][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:57.145][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 21:11:57.146][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:57.147][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 21:11:57.148][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:57.149][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-05-03 21:11:57.150][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-03 21:11:57.151][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 21:11:57.152][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:57.153][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-05-03 21:11:57.154][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 21:11:57.155][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-05-03 21:11:57.155][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-05-03 21:11:57.155][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-05-03 21:11:57.155][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-05-03 21:11:57.155][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-05-03 21:11:57.155][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-05-03 21:11:57.155][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-05-03 21:11:57.155][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-05-03 21:11:57.155][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-05-03 21:11:57.155][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-05-03 21:11:57.155][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-05-03 21:11:57.156][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-03 21:11:57.157][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-03 21:11:57.157][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-03 21:11:57.157][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-03 21:11:57.158][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-03 21:11:57.159][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:11:57.160][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:11:57.161][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 21:11:57.162][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 21:11:57.163][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 21:11:57.164][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 21:11:57.165][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 21:11:57.165][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-05-03 21:11:57.166][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 21:11:57.167][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 21:11:57.168][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-03 21:11:57.169][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-05-03 21:11:57.169][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-05-03 21:11:57.170][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-03 21:11:57.172][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-03 21:11:57.174][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-05-03 21:11:57.175][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-03 21:11:57.177][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-03 21:11:57.179][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-03 21:11:57.183][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-05-03 21:11:57.184][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-05-03 21:11:57.185][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-05-03 21:11:57.187][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-05-03 21:11:57.188][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-03 21:11:57.189][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-03 21:11:57.191][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-05-03 21:11:57.192][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-05-03 21:11:57.193][biodb::testThat]
biodb.INFO [2024-05-03 21:11:57.194][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-05-03 21:11:57.195][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 21:11:57.196][biodb::testThat]
biodb.DEBUG[2024-05-03 21:11:57.201][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-05-03 21:11:57.205][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 21:11:57.206][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-05-03 21:11:57.208][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 21:11:57.209][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-05-03 21:11:57.213][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-03 21:11:57.217][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 21:11:57.218][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-05-03 21:11:57.219][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 21:11:57.221][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-05-03 21:11:57.226][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-05-03 21:11:57.227][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 21:11:57.229][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-05-03 21:11:57.230][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 21:11:57.231][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 21:11:57.232][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 21:11:57.233][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 21:11:57.234][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 21:11:57.235][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 21:11:57.238][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:57.239][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:57.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:57.245][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:57.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:57.247][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:57.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 21:11:57.249][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-05-03 21:11:57.252][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 21:11:57.253][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 21:11:57.254][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-05-03 21:11:57.715][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2024-05-03 21:11:58.972][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 21:11:58.977][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-05-03 21:11:58.985][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-05-03 21:11:58.991][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-05-03 21:11:58.995][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 21:11:58.998][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 21:11:59.001][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 21:11:59.005][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 21:11:59.007][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:59.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:59.019][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:59.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:59.023][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:59.025][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.TRACE[2024-05-03 21:11:59.033][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:59.035][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:59.036][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:59.038][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:59.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:59.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:59.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:59.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:59.062][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:59.063][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:59.064][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:59.065][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:59.067][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 21:11:59.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 21:11:59.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:59.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:59.071][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:59.072][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:59.073][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:59.074][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:59.076][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 21:11:59.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 21:11:59.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:59.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:59.080][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 21:11:59.081][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 21:11:59.082][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:59.083][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:59.084][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 21:11:59.085][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 21:11:59.086][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:59.087][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:59.089][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:59.090][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:59.091][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:59.092][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:59.093][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:59.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 21:11:59.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:59.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:59.097][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:59.098][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:59.099][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:59.100][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:59.102][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 21:11:59.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 21:11:59.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:59.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:59.106][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:59.107][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:59.108][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:59.109][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:59.110][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:59.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 21:11:59.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:59.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:59.114][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:59.115][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:59.116][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:59.117][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:59.119][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 21:11:59.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 21:11:59.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:59.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:59.123][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:59.124][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:59.125][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:59.126][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:59.127][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 21:11:59.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 21:11:59.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:59.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:59.131][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:59.132][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:59.133][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:59.134][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:59.136][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 21:11:59.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 21:11:59.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:59.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:59.153][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:59.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:59.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:59.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:59.157][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:59.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:59.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:59.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:59.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:59.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:59.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:59.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:59.164][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 21:11:59.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 21:11:59.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:59.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:59.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:59.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:59.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:59.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:59.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:59.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:59.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:59.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:59.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:59.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:59.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:59.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:59.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:59.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:59.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:59.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:59.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:59.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:59.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:59.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 21:11:59.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 21:11:59.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 21:11:59.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 21:11:59.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 21:11:59.192][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-05-03 21:11:59.195][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-03 21:11:59.196][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-05-03 21:11:59.197][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-05-03 21:11:59.198][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-03 21:11:59.199][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 21:11:59.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 21:11:59.201][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 21:11:59.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 21:11:59.202][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 21:11:59.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
> 
> proc.time()
   user  system elapsed 
 26.140   1.137  66.480 

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

nameusersystemelapsed
ChebiConn 0.966 0.09361.501
ChebiEntry0.3200.0211.239