| Back to Build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-09-06 08:10 -0400 (Fri, 06 Sep 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4711 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 201/2258 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.11.0 (landing page) Pierrick Roger
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
|
To the developers/maintainers of the biodbChebi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbChebi.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: biodbChebi |
| Version: 1.11.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings biodbChebi_1.11.0.tar.gz |
| StartedAt: 2024-09-05 23:04:47 -0400 (Thu, 05 Sep 2024) |
| EndedAt: 2024-09-05 23:06:36 -0400 (Thu, 05 Sep 2024) |
| EllapsedTime: 109.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbChebi.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings biodbChebi_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.11.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
biodbChebi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘biodbChebi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbChebi)
biodbChebi.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2024-09-05 23:05:29.569][biodb::testContext]
biodb.INFO [2024-09-05 23:05:29.571][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-05 23:05:29.572][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-09-05 23:05:29.573][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-05 23:05:29.574][biodb::testContext]
biodb.INFO [2024-09-05 23:05:29.582][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-09-05 23:05:29.584][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-09-05 23:05:29.592][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-05 23:05:29.593][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-09-05 23:05:29.594][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-09-05 23:05:29.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:29.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:29.598][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-09-05 23:05:29.619][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-09-05 23:05:29.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:29.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:29.623][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-09-05 23:05:29.624][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-09-05 23:05:29.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:29.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:29.628][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-09-05 23:05:29.629][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-09-05 23:05:29.630][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-09-05 23:05:29.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:29.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:29.634][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-09-05 23:05:29.635][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-09-05 23:05:29.636][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-09-05 23:05:29.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:29.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:29.640][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-09-05 23:05:29.641][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-09-05 23:05:29.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:29.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:29.645][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-09-05 23:05:29.646][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-09-05 23:05:29.647][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-09-05 23:05:29.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:29.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:29.651][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-09-05 23:05:29.652][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-09-05 23:05:29.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:29.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.654][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[2024-09-05 23:05:29.655][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-09-05 23:05:29.656][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-09-05 23:05:29.658][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-09-05 23:05:29.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:29.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:29.661][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-09-05 23:05:29.662][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-09-05 23:05:29.663][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-09-05 23:05:29.664][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-09-05 23:05:29.665][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-09-05 23:05:29.666][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-09-05 23:05:29.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:29.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:29.670][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-09-05 23:05:29.671][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-09-05 23:05:29.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:29.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:29.675][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-09-05 23:05:29.676][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-09-05 23:05:29.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:29.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:29.680][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-09-05 23:05:29.681][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-09-05 23:05:29.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:29.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:29.684][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-09-05 23:05:29.686][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-09-05 23:05:29.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:29.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.688][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.DEBUG[2024-09-05 23:05:29.695][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-09-05 23:05:29.696][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-09-05 23:05:29.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:29.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:29.700][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-09-05 23:05:29.701][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-09-05 23:05:29.705][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-09-05 23:05:29.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:29.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:29.709][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-09-05 23:05:29.710][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-09-05 23:05:29.711][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-09-05 23:05:29.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:29.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:29.718][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-09-05 23:05:29.757][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-05 23:05:29.796][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-09-05 23:05:29.797][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-05 23:05:29.798][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-05 23:05:29.799][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-05 23:05:29.801][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-05 23:05:29.802][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-05 23:05:29.803][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-05 23:05:29.804][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-05 23:05:29.805][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-05 23:05:29.806][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-05 23:05:29.807][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-09-05 23:05:29.808][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-05 23:05:29.809][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:05:29.810][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-05 23:05:29.811][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-05 23:05:29.811][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-05 23:05:29.811][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-05 23:05:29.811][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-05 23:05:29.811][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-05 23:05:29.812][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-05 23:05:29.814][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:05:29.815][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:05:29.816][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-05 23:05:29.817][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:05:29.817][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:05:29.818][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-05 23:05:29.819][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:05:29.820][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-05 23:05:29.821][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-05 23:05:29.822][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-05 23:05:29.824][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:05:29.825][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-09-05 23:05:29.827][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-05 23:05:29.828][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-09-05 23:05:29.829][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-05 23:05:29.830][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-05 23:05:29.831][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-05 23:05:29.832][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-05 23:05:29.833][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-05 23:05:29.834][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-05 23:05:29.835][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-05 23:05:29.836][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-05 23:05:29.837][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-05 23:05:29.838][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-09-05 23:05:29.839][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-05 23:05:29.840][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:05:29.841][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-05 23:05:29.842][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-05 23:05:29.842][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-05 23:05:29.842][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-05 23:05:29.842][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-05 23:05:29.842][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-05 23:05:29.843][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-05 23:05:29.844][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:05:29.845][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:05:29.846][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-05 23:05:29.847][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:05:29.848][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:05:29.849][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-05 23:05:29.850][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:05:29.851][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-05 23:05:29.852][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-05 23:05:29.853][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-05 23:05:29.854][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:05:29.855][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-09-05 23:05:29.857][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-05 23:05:29.858][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-09-05 23:05:29.859][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-05 23:05:29.860][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-05 23:05:29.861][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-05 23:05:29.862][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-05 23:05:29.863][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-05 23:05:29.864][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-05 23:05:29.865][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-05 23:05:29.866][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-05 23:05:29.867][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-05 23:05:29.868][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-09-05 23:05:29.869][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-05 23:05:29.870][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:05:29.871][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-05 23:05:29.872][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:05:29.873][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-05 23:05:29.874][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:05:29.875][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:05:29.876][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-05 23:05:29.877][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:05:29.878][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:05:29.879][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-05 23:05:29.880][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:05:29.881][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-05 23:05:29.881][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-05 23:05:29.882][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-05 23:05:29.883][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:05:29.885][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-09-05 23:05:29.886][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-05 23:05:29.887][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-09-05 23:05:29.888][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-05 23:05:29.889][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-05 23:05:29.890][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-05 23:05:29.891][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-05 23:05:29.892][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-05 23:05:29.893][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-05 23:05:29.894][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-05 23:05:29.895][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-05 23:05:29.897][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-05 23:05:29.898][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-09-05 23:05:29.899][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-05 23:05:29.900][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:05:29.901][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-05 23:05:29.902][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:05:29.903][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-05 23:05:29.904][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:05:29.905][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:05:29.906][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-05 23:05:29.907][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:05:29.907][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:05:29.908][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-05 23:05:29.909][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:05:29.910][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-05 23:05:29.911][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-05 23:05:29.912][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-05 23:05:29.913][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:05:29.917][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-05 23:05:29.918][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:29.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:29.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:29.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:29.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:29.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:29.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:29.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:29.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:29.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:29.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:29.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:29.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:29.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:29.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:29.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:29.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.936][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[2024-09-05 23:05:29.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:29.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:29.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:29.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:29.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:29.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:29.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:29.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:29.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:29.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:29.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:29.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.949][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[2024-09-05 23:05:29.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:29.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:29.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:29.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.953][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[2024-09-05 23:05:29.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:29.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:29.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:29.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:29.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:29.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:29.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:29.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:29.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:29.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:29.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:29.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:29.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:29.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:29.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:29.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:29.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:29.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:29.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:29.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:29.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:29.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:29.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:29.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:29.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:29.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:29.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:29.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:29.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:29.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:29.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:29.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.987][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[2024-09-05 23:05:29.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:29.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:29.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:29.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:29.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:29.992][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-09-05 23:05:29.997][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-09-05 23:05:29.998][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-09-05 23:05:29.999][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-09-05 23:05:30.001][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-09-05 23:05:30.002][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-09-05 23:05:30.003][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-09-05 23:05:30.005][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-09-05 23:05:30.006][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-09-05 23:05:30.007][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-09-05 23:05:30.008][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-05 23:05:30.010][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-09-05 23:05:30.011][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-09-05 23:05:30.012][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-09-05 23:05:30.013][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-09-05 23:05:30.015][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-09-05 23:05:30.016][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-09-05 23:05:30.017][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-09-05 23:05:30.019][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-09-05 23:05:30.020][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-09-05 23:05:30.021][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-09-05 23:05:30.022][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-09-05 23:05:30.024][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-09-05 23:05:30.025][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-09-05 23:05:30.026][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-09-05 23:05:30.028][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-09-05 23:05:30.029][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-09-05 23:05:30.030][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-09-05 23:05:30.031][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-09-05 23:05:30.033][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-09-05 23:05:30.034][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-09-05 23:05:30.035][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-09-05 23:05:30.037][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-09-05 23:05:30.038][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-09-05 23:05:30.039][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-09-05 23:05:30.041][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-09-05 23:05:30.047][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-09-05 23:05:30.049][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-09-05 23:05:30.050][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-09-05 23:05:30.051][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-09-05 23:05:30.053][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-09-05 23:05:30.054][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-09-05 23:05:30.055][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-09-05 23:05:30.056][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-09-05 23:05:30.058][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-09-05 23:05:30.059][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-09-05 23:05:30.060][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-09-05 23:05:30.061][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-09-05 23:05:30.063][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-09-05 23:05:30.064][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-09-05 23:05:30.065][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-09-05 23:05:30.066][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-09-05 23:05:30.068][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-09-05 23:05:30.069][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-09-05 23:05:30.070][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-09-05 23:05:30.072][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-09-05 23:05:30.073][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-09-05 23:05:30.074][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-09-05 23:05:30.075][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-09-05 23:05:30.077][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-09-05 23:05:30.078][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-09-05 23:05:30.079][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-09-05 23:05:30.080][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-09-05 23:05:30.082][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-09-05 23:05:30.083][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-09-05 23:05:30.084][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-09-05 23:05:30.086][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-09-05 23:05:30.087][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-09-05 23:05:30.088][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-09-05 23:05:30.089][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-09-05 23:05:30.091][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-09-05 23:05:30.092][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-09-05 23:05:30.093][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-09-05 23:05:30.094][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-09-05 23:05:30.096][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-09-05 23:05:30.097][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-09-05 23:05:30.098][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-09-05 23:05:30.099][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-09-05 23:05:30.101][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-09-05 23:05:30.102][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-09-05 23:05:30.103][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-09-05 23:05:30.105][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-09-05 23:05:30.106][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-09-05 23:05:30.112][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-09-05 23:05:30.113][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-09-05 23:05:30.117][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-05 23:05:30.118][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:30.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:30.119][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:30.120][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[2024-09-05 23:05:30.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:30.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:30.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:30.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:30.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:30.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:30.130][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[2024-09-05 23:05:30.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:30.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:30.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:30.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:30.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:30.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:30.136][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[2024-09-05 23:05:30.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:30.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:30.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:30.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:30.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:30.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:30.142][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[2024-09-05 23:05:30.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:30.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:30.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:30.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:30.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:30.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:30.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:30.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:30.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:30.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:30.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:30.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:30.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:30.153][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.DEBUG[2024-09-05 23:05:30.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:30.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:30.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:30.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:30.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:30.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:30.159][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[2024-09-05 23:05:30.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:30.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:30.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:30.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:30.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:30.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:30.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:30.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:30.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:30.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:30.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:30.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:30.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:30.171][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[2024-09-05 23:05:30.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:30.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:30.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:30.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:30.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:30.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:30.177][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[2024-09-05 23:05:30.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:30.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:30.180][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:30.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:30.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:30.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:30.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:30.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:30.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:30.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:30.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:30.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:30.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:30.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:30.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:30.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:30.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:30.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:30.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:30.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:30.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:30.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:30.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:30.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:30.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:30.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:30.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:30.200][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.DEBUG[2024-09-05 23:05:30.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:30.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:30.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:30.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:30.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:30.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:30.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:30.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:30.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:30.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:30.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:30.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:30.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:30.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:30.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:30.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:30.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:30.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:30.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:30.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:30.220][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[2024-09-05 23:05:30.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:05:30.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:30.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:30.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:30.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:30.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:30.226][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.DEBUG[2024-09-05 23:05:30.228][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-09-05 23:05:30.238][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-09-05 23:05:30.240][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-05 23:05:30.241][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-09-05 23:05:30.242][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-05 23:05:30.243][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-05 23:05:30.244][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-05 23:05:30.245][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-05 23:05:30.246][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-09-05 23:05:30.247][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-09-05 23:05:30.248][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-09-05 23:05:30.249][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-05 23:05:30.250][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-05 23:05:30.251][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-09-05 23:05:30.251][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-05 23:05:30.252][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-09-05 23:05:30.252][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-09-05 23:05:30.252][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-09-05 23:05:30.252][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-09-05 23:05:30.252][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-09-05 23:05:30.252][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-09-05 23:05:30.252][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-09-05 23:05:30.252][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-09-05 23:05:30.252][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-09-05 23:05:30.252][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-09-05 23:05:30.252][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-09-05 23:05:30.254][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-09-05 23:05:30.255][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-05 23:05:30.255][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-05 23:05:30.255][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-05 23:05:30.255][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-09-05 23:05:30.256][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:05:30.257][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:05:30.258][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-05 23:05:30.259][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:05:30.260][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:05:30.261][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-05 23:05:30.262][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-05 23:05:30.262][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-09-05 23:05:30.263][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-05 23:05:30.264][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-05 23:05:30.265][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-09-05 23:05:30.265][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-09-05 23:05:30.265][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-09-05 23:05:30.272][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-09-05 23:05:30.273][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-05 23:05:30.275][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-09-05 23:05:30.276][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-09-05 23:05:30.277][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-09-05 23:05:30.279][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-09-05 23:05:30.310][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-09-05 23:05:30.311][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-09-05 23:05:30.316][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-09-05 23:05:30.320][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-09-05 23:05:30.325][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-05 23:05:30.326][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-05 23:05:30.327][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-09-05 23:05:30.328][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-09-05 23:05:30.339][biodb::testThat]
biodb.INFO [2024-09-05 23:05:30.340][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-09-05 23:05:30.341][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-05 23:05:30.342][biodb::testThat]
biodb.TRACE[2024-09-05 23:05:30.346][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-09-05 23:05:30.348][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-05 23:05:30.351][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-05 23:05:30.361][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:30.362][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:30.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:30.376][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:30.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:30.377][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:30.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:30.388][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:30.390][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:30.391][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.391][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.394][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:30.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:30.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.409][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:30.410][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:30.411][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.412][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.438][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:30.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:30.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.442][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:30.443][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:30.444][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.445][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.446][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:30.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:30.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.450][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:30.451][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:30.452][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.453][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.454][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:30.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:30.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.458][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:30.459][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:30.460][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.461][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.462][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:30.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:30.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.466][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:30.467][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:30.467][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.468][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.470][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:30.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:30.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.473][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:30.474][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:30.475][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.476][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.477][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:30.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:30.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.481][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:30.482][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:30.483][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.484][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.485][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:30.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:30.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.489][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:30.490][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:30.491][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.491][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.493][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:30.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:30.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.497][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:30.498][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:30.499][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.500][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.501][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:30.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:30.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.505][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:30.506][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:30.507][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.507][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.509][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:30.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:30.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.513][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:30.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:30.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.516][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:30.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:30.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:30.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:30.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.524][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:30.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:30.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:30.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:30.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:30.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:30.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:30.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:30.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:30.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:30.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:30.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:30.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:30.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:30.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:30.595][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-09-05 23:05:30.599][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:30.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:30.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.603][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:30.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:30.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.635][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:30.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:30.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.640][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:30.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:30.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.644][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:30.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:30.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.649][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:30.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:30.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.654][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-05 23:05:30.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-05 23:05:30.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.658][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-05 23:05:30.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-05 23:05:30.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.663][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-09-05 23:05:30.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-09-05 23:05:30.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.667][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-09-05 23:05:30.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-09-05 23:05:30.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:30.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:30.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.712][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:30.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:30.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:30.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:30.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:30.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:30.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:30.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:30.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:30.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:30.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:30.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:30.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:30.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:30.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.749][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:30.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:30.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.754][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:30.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:30.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.758][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:30.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:30.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:30.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:30.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:30.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:30.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:30.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:30.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.784][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:30.785][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:30.786][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.787][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:30.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:30.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.804][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:30.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:30.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.857][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:30.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:30.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.861][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:30.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:30.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.866][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:30.867][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:30.868][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.869][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.870][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:30.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:30.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.883][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:30.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:30.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.887][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:30.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:30.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.892][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:30.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:30.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.896][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:30.897][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:30.898][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.899][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.900][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:30.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:30.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.914][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:30.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:30.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.918][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:30.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:30.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.923][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:30.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:30.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.927][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:30.929][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:30.930][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.931][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.932][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:30.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:30.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.944][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:30.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:30.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.948][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:30.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:30.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.953][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:30.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:30.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.957][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:30.958][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:30.959][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.960][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.961][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:30.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:30.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.974][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:30.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:30.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.978][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:30.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:30.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.982][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:30.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:30.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.986][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:30.987][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:30.988][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.989][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:30.990][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:30.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:30.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:30.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.003][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:31.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:31.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.007][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:31.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:31.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.011][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:31.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:31.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.015][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:31.016][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:31.017][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.018][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.019][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:31.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:31.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.032][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-09-05 23:05:31.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:31.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.036][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-09-05 23:05:31.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:31.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.040][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-09-05 23:05:31.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:31.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.044][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-09-05 23:05:31.045][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:31.046][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.047][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.048][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-09-05 23:05:31.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:31.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.060][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:31.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:31.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.064][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:31.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:31.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.068][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:31.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:31.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.072][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:31.073][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:31.074][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.075][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.076][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:31.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:31.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.088][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:31.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:31.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.092][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:31.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:31.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.103][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:31.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:31.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.107][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:31.108][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:31.109][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.110][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.111][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:31.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:31.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.123][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:31.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:31.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.128][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:31.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:31.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.132][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:31.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:31.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.136][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:31.137][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:31.138][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.139][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.140][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:31.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:31.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.152][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:31.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:31.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.156][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:31.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:31.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.160][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:31.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:31.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.165][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:31.166][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:31.167][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.168][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.169][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:31.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:31.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.182][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:31.183][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:31.184][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.185][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.189][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:31.190][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:31.191][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.192][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.197][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:31.198][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:31.199][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.200][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.204][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:31.205][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:31.206][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.207][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.212][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:31.213][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:31.214][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.215][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.219][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:31.220][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:31.221][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.222][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.226][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:31.228][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:31.229][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.230][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.234][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:31.235][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:31.236][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.237][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.241][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-09-05 23:05:31.243][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:31.244][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.244][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.249][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:31.250][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:31.251][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.252][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.256][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:31.257][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:31.258][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.259][ef$get] fields variable is a list.
biodb.INFO [2024-09-05 23:05:31.267][biodb::testThat]
biodb.INFO [2024-09-05 23:05:31.268][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-09-05 23:05:31.269][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-05 23:05:31.270][biodb::testThat]
biodb.DEBUG[2024-09-05 23:05:31.285][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-09-05 23:05:31.293][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-05 23:05:31.299][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-09-05 23:05:31.301][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:05:31.302][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-09-05 23:05:31.303][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-05 23:05:31.329][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-05 23:05:31.339][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-05 23:05:31.341][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:31.342][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:31.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:31.347][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:31.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:31.349][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:31.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:31.353][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:31.354][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:31.355][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.356][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:31.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:31.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.379][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:31.381][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:31.382][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.383][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.384][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:31.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:31.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.388][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:31.389][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:31.390][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.391][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.393][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:31.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:31.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.397][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:31.398][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:31.399][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.400][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.401][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:31.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:31.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.406][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:31.407][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:31.408][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.409][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.410][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:31.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:31.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.414][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:31.415][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:31.416][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.417][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.419][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:31.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:31.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.423][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:31.424][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:31.425][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.426][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.427][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:31.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:31.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.431][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:31.432][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:31.433][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.434][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.436][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:31.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:31.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.440][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:31.441][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:31.442][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.443][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.444][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:31.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:31.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.448][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:31.449][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:31.450][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.451][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.453][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:31.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:31.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.457][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:31.458][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:31.459][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.460][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.461][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:31.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:31.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.465][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:31.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:31.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:31.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:31.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:31.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:31.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.477][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:31.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:31.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:31.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:31.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:31.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:31.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:31.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:31.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:31.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:31.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:31.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:31.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:31.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:31.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:31.505][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-09-05 23:05:31.506][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-09-05 23:05:31.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-09-05 23:05:31.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.510][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-09-05 23:05:31.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-09-05 23:05:31.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.514][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-09-05 23:05:31.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-09-05 23:05:31.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-09-05 23:05:31.526][biodb::testThat]
biodb.INFO [2024-09-05 23:05:31.528][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-09-05 23:05:31.528][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-05 23:05:31.529][biodb::testThat]
biodb.TRACE[2024-09-05 23:05:31.533][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:31.534][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:31.535][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.536][ef$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:31.537][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-09-05 23:05:31.571][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:31.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:31.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.576][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:31.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:31.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.580][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:31.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:31.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:31.588][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-09-05 23:05:31.593][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-09-05 23:05:31.618][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-05 23:05:31.636][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-09-05 23:05:31.638][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:05:31.639][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-09-05 23:05:31.664][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[2024-09-05 23:05:31.668][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-05 23:05:31.670][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-09-05 23:05:31.671][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:05:31.673][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-09-05 23:05:31.675][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-09-05 23:05:31.688][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:31.690][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:31.691][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.692][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.693][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:31.694][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:31.695][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.696][ef$get] fields variable is a list.
biodb.INFO [2024-09-05 23:05:31.700][biodb::testThat]
biodb.INFO [2024-09-05 23:05:31.701][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-09-05 23:05:31.702][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-05 23:05:31.703][biodb::testThat]
biodb.TRACE[2024-09-05 23:05:31.731][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:31.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:31.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.735][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:31.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:31.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.740][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:31.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:31.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:31.816][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[2024-09-05 23:05:31.820][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-05 23:05:31.822][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-09-05 23:05:31.823][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:05:31.825][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-09-05 23:05:31.846][biodb::testThat]
biodb.INFO [2024-09-05 23:05:31.847][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-09-05 23:05:31.849][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-05 23:05:31.850][biodb::testThat]
biodb.TRACE[2024-09-05 23:05:31.875][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:31.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:31.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.880][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:31.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:31.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.884][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:31.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:31.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.888][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:31.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:31.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.892][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:31.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:31.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.897][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:31.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:31.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.901][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-05 23:05:31.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-05 23:05:31.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.906][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-05 23:05:31.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-05 23:05:31.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.911][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-09-05 23:05:31.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-09-05 23:05:31.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.915][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-09-05 23:05:31.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-09-05 23:05:31.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.940][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:31.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:31.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.945][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:31.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:31.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.949][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:31.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:31.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.953][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:31.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:31.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.958][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:31.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:31.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.962][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:31.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:31.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.967][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-05 23:05:31.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-05 23:05:31.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.971][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-05 23:05:31.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-05 23:05:31.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.976][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-09-05 23:05:31.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-09-05 23:05:31.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:31.980][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-09-05 23:05:31.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-09-05 23:05:31.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:31.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-09-05 23:05:31.991][biodb::testThat]
biodb.INFO [2024-09-05 23:05:31.992][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-09-05 23:05:31.993][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-05 23:05:31.994][biodb::testThat]
biodb.INFO [2024-09-05 23:05:32.005][biodb::testThat]
biodb.INFO [2024-09-05 23:05:32.006][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-09-05 23:05:32.007][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-05 23:05:32.008][biodb::testThat]
biodb.INFO [2024-09-05 23:05:32.017][biodb::testThat]
biodb.INFO [2024-09-05 23:05:32.018][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-09-05 23:05:32.019][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-05 23:05:32.020][biodb::testThat]
biodb.DEBUG[2024-09-05 23:05:32.025][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-09-05 23:05:32.955][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-09-05 23:05:34.099][biodb::testThat]
biodb.INFO [2024-09-05 23:05:34.101][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-09-05 23:05:34.102][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-05 23:05:34.103][biodb::testThat]
biodb.DEBUG[2024-09-05 23:05:34.541][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[2024-09-05 23:05:34.964][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:34.966][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:34.967][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:34.968][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:34.969][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:34.970][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:34.971][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:34.972][ef$get] fields variable is a list.
biodb.INFO [2024-09-05 23:05:34.974][biodb::testThat]
biodb.INFO [2024-09-05 23:05:34.974][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2024-09-05 23:05:34.975][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-05 23:05:34.976][biodb::testThat]
biodb.TRACE[2024-09-05 23:05:34.986][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:34.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:34.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:34.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:34.991][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:34.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:34.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:34.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:34.994][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:34.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:34.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:34.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:35.089][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[2024-09-05 23:05:35.092][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-05 23:05:35.093][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-09-05 23:05:35.094][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:05:35.096][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-09-05 23:05:35.152][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[2024-09-05 23:05:35.155][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-05 23:05:35.157][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-09-05 23:05:35.158][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:05:35.159][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-09-05 23:05:35.172][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-05 23:05:35.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-05 23:05:35.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:35.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:35.179][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:35.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:35.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:35.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:35.183][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:35.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:35.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:35.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:35.187][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:35.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:35.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:35.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:35.190][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:35.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:35.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:35.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:35.194][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:35.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:35.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:35.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:35.204][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[2024-09-05 23:05:35.207][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-05 23:05:35.208][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-09-05 23:05:35.210][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:05:35.211][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-09-05 23:05:35.213][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:35.214][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:35.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:35.219][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:35.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:35.221][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:35.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:35.222][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-09-05 23:05:35.273][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-05 23:05:35.275][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-09-05 23:05:35.276][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-05 23:05:35.277][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-05 23:05:35.278][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-05 23:05:35.279][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-05 23:05:35.280][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-05 23:05:35.281][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-05 23:05:35.283][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:35.284][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:35.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:35.289][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:35.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:35.291][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:35.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:35.292][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-09-05 23:05:35.295][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-05 23:05:35.296][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-05 23:05:35.297][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-09-05 23:05:35.689][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-09-05 23:05:36.094][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-05 23:05:36.100][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-09-05 23:05:36.127][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-09-05 23:05:36.131][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-09-05 23:05:36.133][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-05 23:05:36.136][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-05 23:05:36.138][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-05 23:05:36.141][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:36.143][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:36.144][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:36.153][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:36.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:36.155][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:36.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:36.159][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:36.160][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:36.161][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.162][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:36.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:36.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:36.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:36.167][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:36.168][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:36.169][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.170][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:36.172][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:36.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:36.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:36.176][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:36.177][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:36.178][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.179][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:36.181][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:36.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:36.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:36.185][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:36.186][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:36.187][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.188][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:36.189][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:36.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:36.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:36.193][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:36.194][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:36.195][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.196][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:36.198][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:36.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:36.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:36.202][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:36.203][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:36.204][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.204][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:36.206][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:36.207][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:36.208][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.209][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:36.227][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:36.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:36.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:36.231][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:36.232][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:36.233][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.234][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:36.235][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:36.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:36.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:36.239][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:36.240][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:36.241][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.242][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:36.244][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:36.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:36.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:36.248][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:36.249][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:36.250][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.251][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:36.252][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:36.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:36.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:36.256][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:36.257][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:36.258][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.259][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:36.260][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:36.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:36.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:36.264][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:36.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:36.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:36.268][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:36.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:36.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:36.272][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:36.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:36.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:36.276][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:36.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:36.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:36.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:36.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:36.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:36.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:36.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:36.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:36.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:36.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:36.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:36.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:36.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:36.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:36.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:36.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:36.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:36.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:36.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:36.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:36.303][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-09-05 23:05:36.313][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:36.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:36.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:36.317][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:36.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:36.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:36.321][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:36.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:36.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:36.325][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[2024-09-05 23:05:36.329][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-05 23:05:36.330][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-09-05 23:05:36.331][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:05:36.333][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-09-05 23:05:36.348][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:36.349][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:36.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:36.354][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:36.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:36.355][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:36.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:36.357][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:36.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:36.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:36.361][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:36.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:36.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:36.364][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:36.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:36.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:36.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:36.368][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:36.369][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:36.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:36.374][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:36.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:36.376][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:36.376][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[2024-09-05 23:05:36.377][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-09-05 23:05:36.378][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-05 23:05:36.380][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-09-05 23:05:36.381][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-05 23:05:36.382][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-05 23:05:36.383][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-05 23:05:36.384][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-05 23:05:36.385][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-05 23:05:36.386][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-05 23:05:36.405][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:36.406][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:36.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:36.411][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:36.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:36.413][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:36.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:36.415][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-09-05 23:05:36.430][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-05 23:05:36.431][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-05 23:05:36.445][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-09-05 23:05:36.843][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-09-05 23:05:37.238][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-05 23:05:37.242][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-09-05 23:05:37.248][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-09-05 23:05:37.253][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-09-05 23:05:37.255][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-05 23:05:37.257][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-05 23:05:37.259][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-05 23:05:37.262][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:37.264][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:37.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:37.273][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:37.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:37.276][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:37.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:37.282][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:37.284][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:37.285][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.286][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:37.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:37.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:37.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:37.294][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:37.295][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:37.297][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.298][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:37.299][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:37.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:37.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:37.304][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:37.306][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:37.307][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.308][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:37.309][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:37.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:37.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:37.314][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:37.315][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:37.316][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.317][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:37.318][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:37.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:37.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:37.322][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:37.323][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:37.324][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.325][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:37.326][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:37.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:37.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:37.330][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:37.331][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:37.332][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.333][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:37.334][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:37.336][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:37.336][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.337][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:37.339][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:37.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:37.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:37.343][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:37.344][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:37.345][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.345][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:37.347][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:37.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:37.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:37.351][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:37.352][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:37.353][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.354][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:37.355][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:37.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:37.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:37.359][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:37.360][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:37.361][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.362][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:37.364][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:37.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:37.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:37.368][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:37.369][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:37.370][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.371][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:37.377][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:37.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:37.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:37.384][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:37.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:37.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:37.387][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:37.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:37.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:37.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:37.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:37.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:37.395][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:37.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:37.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:37.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:37.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:37.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:37.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:37.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:37.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:37.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:37.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:37.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:37.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:37.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:37.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:37.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:37.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:37.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:37.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:37.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:37.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:37.421][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-09-05 23:05:37.422][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:37.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:37.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:37.425][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:37.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:37.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:37.429][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:37.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:37.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:37.448][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[2024-09-05 23:05:37.451][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-05 23:05:37.452][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-09-05 23:05:37.454][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:05:37.455][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-09-05 23:05:37.458][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:37.459][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:37.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:37.464][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:37.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:37.466][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:37.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:37.468][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:37.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:37.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:37.472][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:37.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:37.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:37.475][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:37.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:37.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:37.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:37.479][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:37.480][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:37.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:37.486][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:37.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:37.488][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:37.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:37.489][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-09-05 23:05:37.490][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-05 23:05:37.492][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-09-05 23:05:37.493][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-05 23:05:37.494][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-05 23:05:37.495][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-05 23:05:37.496][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-05 23:05:37.497][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-05 23:05:37.498][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-05 23:05:37.501][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:37.501][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:37.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:37.507][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:37.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:37.509][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:37.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:37.510][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-09-05 23:05:37.513][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-05 23:05:37.514][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-05 23:05:37.515][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-09-05 23:05:37.902][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-09-05 23:05:38.290][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-05 23:05:38.293][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-09-05 23:05:38.296][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-09-05 23:05:38.298][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-09-05 23:05:38.300][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-05 23:05:38.301][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-05 23:05:38.302][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-05 23:05:38.304][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:38.305][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:38.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:38.310][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:38.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:38.312][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:38.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:38.315][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:38.316][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:38.317][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:38.318][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:38.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:38.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:38.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:38.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:38.331][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:38.332][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:38.333][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:38.334][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:38.335][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:38.336][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:38.337][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:38.338][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:38.339][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:38.340][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:38.341][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:38.342][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:38.343][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:38.344][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:38.345][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:38.346][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:38.347][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:38.348][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:38.349][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:38.350][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:38.351][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:38.352][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:38.353][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:38.353][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:38.355][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:38.355][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:38.356][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:38.357][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:38.358][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:38.359][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:38.360][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:38.361][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:38.362][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:38.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:38.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:38.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:38.366][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:38.367][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:38.368][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:38.368][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:38.370][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:38.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:38.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:38.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:38.373][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:38.374][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:38.375][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:38.376][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:38.377][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:38.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:38.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:38.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:38.381][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:38.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:38.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:38.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:38.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:38.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:38.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:38.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:38.388][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:38.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:38.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:38.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:38.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:38.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:38.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:38.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:38.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:38.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:38.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:38.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:38.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:38.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:38.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:38.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:38.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:38.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:38.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:38.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:38.407][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:38.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:38.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:38.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:38.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:38.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:38.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:38.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:38.414][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-09-05 23:05:38.415][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:38.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:38.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:38.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:38.419][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:38.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:38.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:38.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:38.423][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:38.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:38.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:38.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:38.427][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:38.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:38.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:38.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:38.431][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:38.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:38.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:38.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:38.435][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:38.436][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:38.440][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:38.451][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:38.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:38.453][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:38.454][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[2024-09-05 23:05:38.456][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-09-05 23:05:38.458][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-05 23:05:38.460][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-09-05 23:05:38.462][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-05 23:05:38.463][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-05 23:05:38.464][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-05 23:05:38.465][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-05 23:05:38.467][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-05 23:05:38.468][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-05 23:05:38.473][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:38.474][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:38.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:38.480][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:38.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:38.482][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:38.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:38.484][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-09-05 23:05:38.488][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-05 23:05:38.489][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-05 23:05:38.490][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-09-05 23:05:38.891][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-09-05 23:05:39.325][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-05 23:05:39.332][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-09-05 23:05:39.341][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-09-05 23:05:39.347][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-09-05 23:05:39.350][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-05 23:05:39.353][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-05 23:05:39.357][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-05 23:05:39.361][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:39.363][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:39.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:39.398][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:39.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:39.404][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:39.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:39.408][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:39.410][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:39.411][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:39.412][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:39.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:39.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:39.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:39.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:39.418][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:39.419][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:39.420][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:39.421][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:39.422][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:39.423][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:39.424][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:39.425][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:39.426][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:39.427][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:39.428][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:39.429][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:39.430][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:39.431][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:39.432][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:39.433][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:39.435][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:39.436][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:39.437][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:39.438][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:39.439][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:39.440][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:39.441][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:39.442][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:39.443][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:39.444][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:39.445][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:39.446][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:39.447][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:39.448][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:39.449][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:39.450][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:39.452][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:39.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:39.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:39.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:39.456][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:39.457][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:39.458][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:39.459][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:39.460][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:39.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:39.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:39.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:39.464][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:39.465][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:39.466][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:39.467][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:39.468][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:39.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:39.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:39.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:39.472][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:39.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:39.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:39.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:39.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:39.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:39.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:39.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:39.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:39.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:39.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:39.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:39.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:39.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:39.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:39.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:39.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:39.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:39.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:39.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:39.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:39.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:39.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:39.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:39.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:39.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:39.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:39.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:39.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:39.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:39.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:39.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:39.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:39.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:39.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:39.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:39.513][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-09-05 23:05:39.514][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:39.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:39.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:39.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:39.519][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:39.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:39.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:39.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:39.524][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:39.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:39.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:39.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:39.528][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:39.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:39.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:39.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:39.532][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:39.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:39.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:39.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:39.535][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:39.536][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:39.537][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:39.541][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:39.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:39.543][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:39.544][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.DEBUG[2024-09-05 23:05:39.545][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-09-05 23:05:39.546][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-05 23:05:39.547][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-09-05 23:05:39.549][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-05 23:05:39.550][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-05 23:05:39.551][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-05 23:05:39.552][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-05 23:05:39.553][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-05 23:05:39.554][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-05 23:05:39.557][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:39.558][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:39.558][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:39.563][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:39.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:39.565][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:39.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:39.567][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-09-05 23:05:39.569][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-05 23:05:39.570][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-05 23:05:39.572][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-09-05 23:05:39.962][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-09-05 23:05:40.391][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-05 23:05:40.393][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-09-05 23:05:40.397][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-09-05 23:05:40.399][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-09-05 23:05:40.412][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-05 23:05:40.413][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-05 23:05:40.414][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-05 23:05:40.416][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:40.417][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:40.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:40.422][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:40.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:40.424][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:40.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:40.428][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:40.429][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:40.430][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:40.431][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:40.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:40.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:40.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:40.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:40.436][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:40.437][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:40.438][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:40.439][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:40.440][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:40.441][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:40.442][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:40.443][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:40.445][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:40.446][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:40.447][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:40.448][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:40.449][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:40.450][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:40.451][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:40.452][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:40.453][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:40.454][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:40.455][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:40.456][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:40.457][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:40.458][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:40.459][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:40.460][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:40.461][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:40.462][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:40.463][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:40.464][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:40.466][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:40.467][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:40.468][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:40.468][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:40.470][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:40.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:40.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:40.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:40.474][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:40.475][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:40.476][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:40.477][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:40.479][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:40.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:40.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:40.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:40.482][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:40.484][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:40.484][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:40.485][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:40.487][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:40.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:40.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:40.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:40.491][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:40.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:40.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:40.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:40.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:40.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:40.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:40.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:40.498][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:40.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:40.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:40.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:40.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:40.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:40.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:40.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:40.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:40.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:40.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:40.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:40.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:40.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:40.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:40.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:40.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:40.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:40.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:40.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:40.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:40.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:40.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:40.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:40.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:40.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:40.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:40.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:40.526][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-09-05 23:05:40.527][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:40.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:40.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:40.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:40.531][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:40.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:40.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:40.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:40.535][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:40.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:40.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:40.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:40.539][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:40.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:40.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:40.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:40.543][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:40.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:40.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:40.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:40.547][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:40.548][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:40.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:40.553][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:40.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:40.555][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:40.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:40.557][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-09-05 23:05:40.558][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-05 23:05:40.560][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-09-05 23:05:40.561][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-05 23:05:40.562][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-05 23:05:40.563][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-05 23:05:40.564][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-05 23:05:40.565][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-05 23:05:40.566][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-05 23:05:40.569][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:40.570][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:40.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:40.576][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:40.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:40.578][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:40.579][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[2024-09-05 23:05:40.580][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-09-05 23:05:40.583][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-05 23:05:40.584][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-05 23:05:40.591][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-09-05 23:05:40.977][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-09-05 23:05:41.362][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-05 23:05:41.365][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-09-05 23:05:41.368][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-09-05 23:05:41.371][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-09-05 23:05:41.372][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-05 23:05:41.374][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-05 23:05:41.375][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-05 23:05:41.377][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:41.378][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:41.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:41.383][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:41.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:41.385][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:41.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:41.389][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:41.390][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:41.391][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.391][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:41.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:41.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:41.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:41.397][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:41.398][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:41.399][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.400][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:41.401][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:41.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:41.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:41.405][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:41.406][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:41.407][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.408][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:41.416][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:41.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:41.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:41.421][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:41.422][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:41.423][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.424][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:41.426][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:41.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:41.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:41.430][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:41.431][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:41.432][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.433][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:41.434][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:41.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:41.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:41.438][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:41.439][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:41.440][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.441][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:41.443][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:41.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:41.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:41.447][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:41.448][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:41.449][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.450][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:41.451][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:41.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:41.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:41.455][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:41.456][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:41.458][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.458][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:41.460][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:41.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:41.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:41.464][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:41.465][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:41.466][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.467][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:41.469][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:41.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:41.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:41.473][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:41.474][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:41.475][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.476][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:41.477][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:41.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:41.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:41.481][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:41.482][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:41.483][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.484][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:41.485][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:41.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:41.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:41.490][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:41.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:41.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:41.494][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:41.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:41.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:41.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:41.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:41.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:41.502][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:41.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:41.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:41.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:41.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:41.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:41.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:41.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:41.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:41.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:41.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:41.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:41.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:41.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:41.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:41.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:41.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:41.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:41.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:41.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:41.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:41.530][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-09-05 23:05:41.531][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:41.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:41.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:41.535][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:41.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:41.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:41.539][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:41.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:41.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:41.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:41.543][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:41.566][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:41.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:41.573][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:41.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:41.574][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:41.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:41.577][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-09-05 23:05:41.578][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-05 23:05:41.580][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-09-05 23:05:41.581][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-05 23:05:41.582][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-05 23:05:41.583][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-05 23:05:41.584][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-05 23:05:41.585][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-05 23:05:41.586][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-05 23:05:41.589][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:41.590][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:41.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:41.596][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:41.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:41.598][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:41.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:41.600][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-09-05 23:05:41.603][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-05 23:05:41.604][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-05 23:05:41.605][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-09-05 23:05:41.995][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-09-05 23:05:42.425][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-05 23:05:42.429][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-09-05 23:05:42.435][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-09-05 23:05:42.439][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-09-05 23:05:42.441][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-05 23:05:42.443][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-05 23:05:42.445][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-05 23:05:42.447][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:42.448][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:42.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:42.454][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:42.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:42.456][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:42.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:42.460][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:42.461][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:42.462][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.462][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:42.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:42.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:42.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:42.468][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:42.469][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:42.469][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.470][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:42.472][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:42.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:42.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:42.476][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:42.477][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:42.477][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.478][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:42.480][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:42.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:42.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:42.484][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:42.485][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:42.485][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.486][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:42.488][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:42.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:42.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:42.491][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:42.492][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:42.493][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.494][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:42.496][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:42.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:42.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:42.499][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:42.500][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:42.501][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.502][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:42.503][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:42.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:42.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:42.507][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:42.509][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:42.510][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.510][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:42.512][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:42.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:42.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:42.516][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:42.517][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:42.518][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.519][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:42.520][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:42.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:42.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:42.524][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:42.525][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:42.526][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.527][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:42.528][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:42.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:42.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:42.532][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:42.533][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:42.534][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.535][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:42.536][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:42.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:42.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:42.541][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:42.542][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:42.543][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.543][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:42.545][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:42.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:42.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:42.549][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:42.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:42.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:42.553][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:42.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:42.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:42.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:42.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:42.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:42.560][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:42.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:42.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:42.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:42.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:42.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:42.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:42.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:42.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:42.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:42.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:42.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:42.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:42.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:42.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:42.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:42.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:42.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:42.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:42.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:42.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:42.602][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-09-05 23:05:42.603][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:42.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:42.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:42.607][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:42.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:42.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:42.611][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:42.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:42.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:42.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:42.615][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:42.615][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:42.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:42.621][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:42.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:42.623][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:42.623][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[2024-09-05 23:05:42.625][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-09-05 23:05:42.626][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-05 23:05:42.627][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-09-05 23:05:42.629][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-05 23:05:42.630][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-05 23:05:42.631][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-05 23:05:42.632][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-05 23:05:42.633][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-05 23:05:42.634][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-05 23:05:42.637][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:42.638][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:42.639][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:42.643][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:42.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:42.645][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:42.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:42.647][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-09-05 23:05:42.650][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-05 23:05:42.651][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-05 23:05:42.652][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-09-05 23:05:43.037][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-09-05 23:05:43.428][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-05 23:05:43.432][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-09-05 23:05:43.439][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-09-05 23:05:43.444][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-09-05 23:05:43.448][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-05 23:05:43.450][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-05 23:05:43.453][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-05 23:05:43.456][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:43.458][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:43.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:43.469][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:43.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:43.473][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:43.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:43.479][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:43.480][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:43.482][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:43.484][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:43.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:43.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:43.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:43.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:43.491][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:43.493][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:43.494][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:43.495][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:43.497][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:43.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:43.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:43.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:43.502][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:43.504][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:43.505][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:43.506][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:43.507][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:43.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:43.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:43.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:43.512][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:43.513][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:43.514][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:43.515][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:43.516][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:43.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:43.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:43.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:43.520][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:43.521][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:43.522][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:43.523][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:43.524][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:43.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:43.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:43.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:43.528][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:43.529][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:43.530][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:43.531][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:43.532][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:43.533][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:43.534][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:43.535][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:43.536][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:43.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:43.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:43.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:43.540][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:43.541][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:43.542][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:43.543][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:43.544][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:43.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:43.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:43.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:43.547][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:43.548][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:43.549][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:43.550][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:43.551][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:43.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:43.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:43.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:43.555][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:43.556][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:43.557][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:43.565][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:43.567][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:43.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:43.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:43.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:43.570][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:43.571][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:43.572][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:43.573][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:43.574][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:43.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:43.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:43.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:43.578][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:43.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:43.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:43.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:43.582][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:43.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:43.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:43.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:43.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:43.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:43.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:43.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:43.589][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:43.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:43.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:43.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:43.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:43.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:43.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:43.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:43.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:43.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:43.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:43.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:43.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:43.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:43.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:43.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:43.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:43.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:43.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:43.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:43.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:43.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:43.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:43.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:43.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:43.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:43.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:43.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:43.615][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-09-05 23:05:43.616][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:43.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:43.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:43.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:43.619][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:43.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:43.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:43.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:43.623][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:43.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:43.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:43.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:43.627][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:43.627][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:43.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:43.633][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:43.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:43.634][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:43.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:43.636][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-09-05 23:05:43.637][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-05 23:05:43.639][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-09-05 23:05:43.640][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-05 23:05:43.641][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-05 23:05:43.642][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-05 23:05:43.643][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-05 23:05:43.644][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-05 23:05:43.645][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-05 23:05:43.648][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:43.649][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:43.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:43.654][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:43.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:43.656][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:43.657][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[2024-09-05 23:05:43.658][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-09-05 23:05:43.661][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-05 23:05:43.662][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-05 23:05:43.663][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-09-05 23:05:44.047][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-09-05 23:05:44.449][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-05 23:05:44.451][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-09-05 23:05:44.454][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-09-05 23:05:44.457][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-09-05 23:05:44.458][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-05 23:05:44.459][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-05 23:05:44.460][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-05 23:05:44.462][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:44.463][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:44.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:44.468][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:44.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:44.470][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:44.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:44.473][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:44.474][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:44.475][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:44.476][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:44.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:44.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:44.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:44.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:44.482][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:44.483][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:44.484][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:44.485][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:44.486][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:44.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:44.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:44.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:44.490][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:44.491][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:44.492][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:44.493][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:44.494][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:44.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:44.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:44.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:44.498][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:44.499][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:44.500][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:44.501][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:44.503][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:44.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:44.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:44.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:44.506][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:44.507][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:44.508][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:44.509][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:44.510][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:44.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:44.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:44.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:44.519][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:44.523][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:44.524][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:44.525][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:44.526][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:44.527][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:44.528][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:44.529][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:44.530][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:44.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:44.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:44.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:44.534][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:44.535][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:44.536][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:44.537][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:44.538][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:44.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:44.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:44.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:44.542][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:44.543][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:44.544][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:44.544][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:44.546][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:44.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:44.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:44.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:44.550][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:44.551][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:44.551][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:44.552][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:44.554][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:44.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:44.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:44.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:44.558][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:44.558][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:44.559][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:44.560][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:44.561][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:44.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:44.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:44.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:44.565][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:44.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:44.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:44.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:44.569][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:44.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:44.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:44.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:44.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:44.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:44.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:44.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:44.576][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:44.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:44.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:44.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:44.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:44.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:44.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:44.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:44.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:44.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:44.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:44.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:44.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:44.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:44.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:44.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:44.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:44.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:44.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:44.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:44.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:44.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:44.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:44.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:44.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:44.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:44.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:44.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:44.602][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-09-05 23:05:44.603][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:44.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:44.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:44.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:44.607][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:44.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:44.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:44.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:44.611][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:44.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:44.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:44.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:44.614][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:44.615][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:44.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:44.620][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:44.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:44.622][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:44.623][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[2024-09-05 23:05:44.624][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-09-05 23:05:44.625][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-05 23:05:44.627][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-09-05 23:05:44.628][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-05 23:05:44.629][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-05 23:05:44.630][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-05 23:05:44.631][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-05 23:05:44.632][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-05 23:05:44.633][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-05 23:05:44.636][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:44.637][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:44.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:44.643][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:44.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:44.645][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:44.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:44.647][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-09-05 23:05:44.650][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-05 23:05:44.650][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-05 23:05:44.652][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-09-05 23:05:45.050][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-09-05 23:05:45.464][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-05 23:05:45.467][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-09-05 23:05:45.471][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-09-05 23:05:45.474][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-09-05 23:05:45.475][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-05 23:05:45.477][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-05 23:05:45.478][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-05 23:05:45.481][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:45.482][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:45.483][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:45.489][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:45.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:45.491][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:45.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:45.494][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:45.496][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:45.497][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:45.498][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:45.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:45.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:45.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:45.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:45.503][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:45.524][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:45.525][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:45.526][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:45.527][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:45.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:45.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:45.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:45.532][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:45.533][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:45.534][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:45.535][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:45.536][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:45.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:45.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:45.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:45.540][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:45.542][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:45.543][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:45.544][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:45.545][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:45.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:45.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:45.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:45.549][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:45.550][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:45.551][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:45.552][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:45.553][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:45.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:45.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:45.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:45.558][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:45.559][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:45.560][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:45.561][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:45.562][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:45.563][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:45.564][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:45.565][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:45.566][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:45.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:45.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:45.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:45.571][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:45.572][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:45.573][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:45.574][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:45.575][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:45.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:45.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:45.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:45.579][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:45.580][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:45.581][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:45.582][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:45.584][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:45.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:45.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:45.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:45.588][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:45.589][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:45.590][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:45.591][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:45.593][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:45.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:45.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:45.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:45.597][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:45.598][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:45.599][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:45.600][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:45.601][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:45.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:45.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:45.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:45.606][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:45.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:45.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:45.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:45.610][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:45.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:45.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:45.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:45.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:45.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:45.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:45.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:45.618][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:45.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:45.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:45.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:45.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:45.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:45.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:45.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:45.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:45.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:45.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:45.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:45.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:45.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:45.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:45.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:45.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:45.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:45.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:45.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:45.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:45.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:45.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:45.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:45.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:45.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:45.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:45.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:45.647][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-09-05 23:05:45.648][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:45.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:45.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:45.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:45.652][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:45.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:45.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:45.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:45.656][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:45.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:45.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:45.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:45.660][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:45.661][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:45.662][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:45.667][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:45.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:45.669][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:45.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:45.670][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-09-05 23:05:45.671][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-05 23:05:45.673][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-09-05 23:05:45.674][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-05 23:05:45.675][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-05 23:05:45.676][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-05 23:05:45.677][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-05 23:05:45.678][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-05 23:05:45.679][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-05 23:05:45.682][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:45.683][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:45.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:45.688][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:45.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:45.690][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:45.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:45.692][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-09-05 23:05:45.695][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-05 23:05:45.696][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-05 23:05:45.697][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-09-05 23:05:46.110][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-09-05 23:05:46.506][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-05 23:05:46.509][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-09-05 23:05:46.512][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-09-05 23:05:46.514][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-09-05 23:05:46.516][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-05 23:05:46.517][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-05 23:05:46.518][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-05 23:05:46.520][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:46.521][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:46.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:46.526][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:46.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:46.528][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:46.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:46.531][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:46.532][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:46.533][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:46.534][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:46.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:46.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:46.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:46.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:46.540][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:46.541][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:46.542][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:46.543][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:46.544][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:46.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:46.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:46.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:46.548][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:46.549][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:46.550][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:46.551][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:46.552][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:46.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:46.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:46.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:46.556][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:46.557][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:46.558][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:46.559][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:46.561][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:46.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:46.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:46.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:46.565][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:46.566][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:46.567][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:46.568][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:46.569][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:46.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:46.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:46.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:46.573][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:46.574][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:46.575][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:46.576][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:46.577][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:46.578][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:46.579][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:46.580][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:46.581][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:46.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:46.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:46.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:46.585][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:46.586][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:46.587][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:46.588][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:46.589][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:46.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:46.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:46.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:46.593][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:46.594][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:46.595][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:46.596][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:46.597][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:46.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:46.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:46.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:46.601][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:46.602][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:46.603][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:46.604][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:46.605][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:46.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:46.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:46.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:46.609][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:46.610][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:46.611][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:46.611][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:46.613][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:46.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:46.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:46.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:46.616][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:46.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:46.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:46.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:46.620][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:46.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:46.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:46.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:46.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:46.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:46.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:46.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:46.628][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:46.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:46.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:46.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:46.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:46.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:46.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:46.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:46.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:46.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:46.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:46.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:46.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:46.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:46.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:46.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:46.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:46.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:46.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:46.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:46.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:46.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:46.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:46.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:46.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:46.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:46.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:46.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:46.657][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-09-05 23:05:46.658][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:46.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:46.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:46.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:46.662][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:46.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:46.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:46.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:46.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:46.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:46.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:46.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:46.670][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:46.671][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:46.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:46.677][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:46.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:46.721][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:46.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:46.723][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-09-05 23:05:46.724][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-05 23:05:46.726][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-09-05 23:05:46.727][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-05 23:05:46.728][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-05 23:05:46.729][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-05 23:05:46.730][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-05 23:05:46.731][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-05 23:05:46.732][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-05 23:05:46.735][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:46.736][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:46.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:46.741][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:46.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:46.743][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:46.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:46.745][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-09-05 23:05:46.748][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-05 23:05:46.749][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-05 23:05:46.750][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-09-05 23:05:47.152][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-09-05 23:05:47.551][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-05 23:05:47.555][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-09-05 23:05:47.559][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-09-05 23:05:47.561][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-09-05 23:05:47.563][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-05 23:05:47.564][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-05 23:05:47.565][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-05 23:05:47.568][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:47.568][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:47.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:47.576][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:47.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:47.577][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:47.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:47.582][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:47.583][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:47.584][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.585][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:47.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:47.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.591][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:47.592][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:47.593][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.594][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.595][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:47.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:47.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.599][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:47.600][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:47.601][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.602][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.604][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:47.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:47.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.608][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:47.609][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:47.610][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.611][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.612][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:47.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:47.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.617][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:47.618][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:47.619][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.619][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.621][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:47.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:47.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.625][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:47.626][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:47.627][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.628][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.629][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:47.630][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:47.631][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.632][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.634][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:47.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:47.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.638][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:47.639][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:47.640][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.641][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.642][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:47.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:47.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.647][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:47.648][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:47.649][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.650][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.651][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:47.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:47.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.655][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:47.656][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:47.657][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.658][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.660][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:47.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:47.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.664][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:47.665][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:47.666][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.667][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.668][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:47.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:47.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.672][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:47.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:47.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.676][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:47.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:47.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:47.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:47.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.684][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:47.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:47.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:47.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:47.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:47.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:47.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:47.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:47.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:47.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:47.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:47.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:47.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:47.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:47.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:47.729][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-09-05 23:05:47.731][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:47.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:47.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.734][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:47.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:47.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.739][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:47.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:47.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:47.743][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:47.743][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:47.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:47.749][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:47.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:47.751][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:47.751][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[2024-09-05 23:05:47.752][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-09-05 23:05:47.753][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-05 23:05:47.755][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-09-05 23:05:47.756][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:05:47.757][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml".
biodb.DEBUG[2024-09-05 23:05:47.758][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-05 23:05:47.760][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-05 23:05:47.761][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-05 23:05:47.762][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:47.763][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:47.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:47.768][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:47.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:47.770][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:47.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:47.773][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:47.774][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:47.774][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.775][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:47.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:47.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.780][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:47.781][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:47.782][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.783][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.784][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:47.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:47.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.788][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:47.789][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:47.790][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.790][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.792][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:47.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:47.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.795][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:47.796][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:47.797][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.798][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.799][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:47.800][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:47.801][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.802][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.803][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:47.804][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:47.805][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.806][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.807][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:47.808][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:47.809][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.809][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.811][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:47.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:47.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.814][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:47.815][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:47.816][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.817][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.818][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:47.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:47.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.822][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:47.823][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:47.824][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.825][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.826][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:47.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:47.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.830][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:47.831][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:47.832][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.833][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.834][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:47.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:47.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.838][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:47.839][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:47.840][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.841][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.842][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:47.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:47.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.845][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:47.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:47.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:47.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:47.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.853][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:47.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:47.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:47.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:47.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:47.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:47.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:47.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:47.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:47.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:47.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:47.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:47.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:47.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:47.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:47.879][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-09-05 23:05:47.880][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:47.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:47.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.890][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:47.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:47.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.894][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:47.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:47.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:47.898][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:47.898][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:47.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:47.904][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:47.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:47.906][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:47.906][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[2024-09-05 23:05:47.907][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-09-05 23:05:47.908][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-05 23:05:47.910][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-09-05 23:05:47.911][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:05:47.912][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml".
biodb.DEBUG[2024-09-05 23:05:47.914][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-05 23:05:47.915][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-05 23:05:47.916][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-05 23:05:47.917][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:47.918][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:47.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:47.923][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:47.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:47.925][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:47.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:47.928][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:47.929][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:47.930][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.931][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:47.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:47.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.936][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:47.937][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:47.938][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.939][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.940][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:47.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:47.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.943][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:47.944][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:47.945][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.946][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.947][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:47.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:47.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.951][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:47.952][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:47.953][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.954][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.955][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:47.956][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:47.957][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.958][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.959][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:47.960][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:47.961][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.962][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.963][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:47.964][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:47.965][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.966][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.967][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:47.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:47.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.971][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:47.972][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:47.973][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.974][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.975][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:47.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:47.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.979][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:47.980][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:47.981][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.982][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.983][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:47.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:47.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.987][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:47.988][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:47.989][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.990][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.991][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:47.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:47.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:47.996][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:47.997][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:47.997][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:47.998][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.000][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.003][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.012][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:48.040][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-09-05 23:05:48.041][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.045][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.048][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:48.052][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:48.053][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:48.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:48.062][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:48.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:48.064][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:48.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:48.066][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-09-05 23:05:48.067][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-05 23:05:48.069][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-09-05 23:05:48.070][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:05:48.071][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml".
biodb.DEBUG[2024-09-05 23:05:48.072][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-05 23:05:48.073][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-05 23:05:48.074][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-05 23:05:48.076][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:48.077][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:48.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:48.082][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:48.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:48.084][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:48.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:48.087][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.088][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.089][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.090][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.091][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.095][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:48.096][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:48.097][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.098][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.099][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:48.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:48.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.103][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:48.104][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:48.105][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.106][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.107][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:48.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:48.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.111][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:48.112][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:48.113][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.114][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.115][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:48.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:48.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.119][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:48.120][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:48.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.121][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.123][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:48.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:48.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.126][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:48.127][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:48.128][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.129][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.130][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:48.131][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.132][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.133][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.134][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:48.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.138][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:48.139][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:48.140][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.141][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.142][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:48.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:48.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.146][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:48.147][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:48.148][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.148][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.150][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:48.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:48.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.154][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:48.155][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:48.156][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.156][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.158][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:48.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:48.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.161][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:48.162][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:48.163][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.164][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.165][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:48.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:48.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.169][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.172][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.180][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:48.205][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-09-05 23:05:48.206][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.210][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.214][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:48.217][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:48.218][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:48.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:48.223][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:48.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:48.230][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:48.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:48.232][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-09-05 23:05:48.233][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-05 23:05:48.235][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-09-05 23:05:48.236][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:05:48.238][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml".
biodb.DEBUG[2024-09-05 23:05:48.239][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-05 23:05:48.240][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-05 23:05:48.241][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-05 23:05:48.242][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:48.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:48.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:48.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:48.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:48.250][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:48.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:48.253][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.254][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.255][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.256][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.261][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:48.262][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:48.262][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.263][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.264][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:48.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:48.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.268][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:48.269][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:48.270][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.271][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.272][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:48.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:48.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.275][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:48.276][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:48.277][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.278][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.279][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:48.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:48.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.283][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:48.284][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:48.285][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.286][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.287][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:48.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:48.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.290][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:48.291][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:48.292][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.293][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.294][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:48.295][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.296][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.297][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.298][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:48.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.302][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:48.303][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:48.304][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.304][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.305][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:48.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:48.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.309][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:48.310][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:48.311][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.312][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.313][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:48.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:48.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.317][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:48.318][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:48.319][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.319][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.320][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:48.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:48.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.324][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:48.325][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:48.326][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.327][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.328][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:48.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:48.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.332][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.335][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.342][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:48.368][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-09-05 23:05:48.369][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.372][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.376][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:48.380][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:48.380][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:48.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:48.385][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:48.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:48.387][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:48.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:48.394][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-09-05 23:05:48.395][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-05 23:05:48.396][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-09-05 23:05:48.397][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:05:48.399][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml".
biodb.DEBUG[2024-09-05 23:05:48.400][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-05 23:05:48.401][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-05 23:05:48.402][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-05 23:05:48.403][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:48.404][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:48.405][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:48.409][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:48.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:48.411][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:48.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:48.414][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.415][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.416][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.417][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.422][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:48.423][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:48.424][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.425][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.426][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:48.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:48.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.429][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:48.430][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:48.431][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.432][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.433][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:48.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:48.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.437][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:48.438][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:48.439][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.440][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.441][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:48.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:48.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.444][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:48.445][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:48.446][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.447][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.448][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:48.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:48.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.452][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:48.453][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:48.454][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.455][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.456][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:48.457][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.458][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.458][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.460][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:48.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.463][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:48.464][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:48.465][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.466][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.467][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:48.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:48.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.471][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:48.472][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:48.473][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.473][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.475][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:48.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:48.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.478][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:48.479][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:48.480][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.481][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.482][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:48.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:48.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.486][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:48.487][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:48.488][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.488][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.490][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:48.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:48.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.493][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.504][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:48.530][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-09-05 23:05:48.531][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.535][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.539][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:48.542][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:48.543][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:48.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:48.549][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:48.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:48.550][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:48.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:48.557][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-09-05 23:05:48.559][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-05 23:05:48.560][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-09-05 23:05:48.561][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:05:48.563][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml".
biodb.DEBUG[2024-09-05 23:05:48.564][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-05 23:05:48.565][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-05 23:05:48.566][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-05 23:05:48.568][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:48.569][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:48.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:48.574][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:48.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:48.576][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:48.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:48.579][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.580][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.580][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.581][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.586][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:48.587][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:48.588][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.589][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.590][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:48.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:48.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.594][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:48.595][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:48.596][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.597][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.598][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:48.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:48.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.602][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:48.603][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:48.604][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.605][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.606][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:48.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:48.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.610][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:48.611][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:48.612][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.613][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.614][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:48.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:48.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.618][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:48.619][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:48.620][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.621][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.622][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:48.623][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.624][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.625][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.626][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:48.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.630][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:48.631][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:48.631][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.632][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.633][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:48.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:48.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.637][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:48.638][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:48.639][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.640][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.641][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:48.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:48.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.645][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:48.646][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:48.647][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.648][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.649][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:48.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:48.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.653][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:48.654][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:48.655][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.656][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.657][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:48.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:48.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.661][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.664][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.672][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:48.698][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-09-05 23:05:48.699][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.703][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.707][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:48.711][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:48.711][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:48.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:48.717][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:48.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:48.718][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:48.719][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[2024-09-05 23:05:48.720][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-09-05 23:05:48.727][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-05 23:05:48.729][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-09-05 23:05:48.730][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:05:48.731][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml".
biodb.DEBUG[2024-09-05 23:05:48.732][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-05 23:05:48.734][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-05 23:05:48.735][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-05 23:05:48.737][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:48.737][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:48.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:48.743][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:48.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:48.745][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:48.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:48.748][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.749][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.750][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.751][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.756][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:48.757][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:48.758][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.759][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.760][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:48.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:48.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.764][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:48.766][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:48.767][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.768][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.769][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:48.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:48.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.773][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:48.774][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:48.775][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.776][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.777][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:48.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:48.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.781][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:48.782][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:48.783][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.783][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.785][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:48.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:48.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.789][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:48.790][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:48.790][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.791][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.792][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:48.793][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.794][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.795][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.796][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:48.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.800][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:48.801][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:48.802][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.803][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.804][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:48.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:48.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.808][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:48.809][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:48.809][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.810][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.812][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:48.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:48.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.815][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:48.816][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:48.817][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.818][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.819][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:48.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:48.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.823][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:48.824][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:48.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.826][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.827][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:48.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:48.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.831][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.835][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:48.870][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-09-05 23:05:48.871][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.874][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.878][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:48.881][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:48.882][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:48.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:48.887][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:48.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:48.889][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:48.890][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[2024-09-05 23:05:48.891][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-09-05 23:05:48.892][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-05 23:05:48.899][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-09-05 23:05:48.901][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:05:48.902][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml".
biodb.DEBUG[2024-09-05 23:05:48.903][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-05 23:05:48.904][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-05 23:05:48.905][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-05 23:05:48.907][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:48.907][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:48.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:48.913][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:48.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:48.914][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:48.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:48.917][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.918][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.919][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.920][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:48.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:48.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.925][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:48.926][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:48.927][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.928][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.929][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:48.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:48.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.933][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:48.934][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:48.935][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.936][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.937][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:48.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:48.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.941][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:48.942][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:48.943][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.943][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.945][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:48.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:48.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.948][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:48.949][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:48.950][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.951][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.952][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:48.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:48.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.956][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:48.957][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:48.958][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.959][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.960][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:48.962][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.962][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.963][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.964][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:48.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:48.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.968][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:48.969][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:48.970][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.971][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.972][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:48.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:48.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.976][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:48.977][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:48.978][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.978][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.980][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:48.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:48.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.983][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:48.984][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:48.985][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.986][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.987][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:48.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:48.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.991][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:48.992][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:48.993][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.994][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.995][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:48.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:48.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:48.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:48.999][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:48.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:49.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.002][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:49.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:49.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:49.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:49.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.009][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:49.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:49.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:49.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:49.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:49.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:49.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:49.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:49.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:49.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:49.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:49.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:49.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:49.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:49.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:49.035][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-09-05 23:05:49.036][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.040][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.044][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:49.047][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:49.048][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:49.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:49.054][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:49.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:49.055][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:49.056][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[2024-09-05 23:05:49.057][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-09-05 23:05:49.058][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-05 23:05:49.065][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-09-05 23:05:49.067][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:05:49.068][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml".
biodb.DEBUG[2024-09-05 23:05:49.069][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-05 23:05:49.070][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-05 23:05:49.072][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-05 23:05:49.073][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:49.074][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:49.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:49.079][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:49.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:49.081][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:49.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:49.084][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:49.085][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:49.086][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.087][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:49.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:49.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.092][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:49.093][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:49.094][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.095][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.096][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:49.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:49.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.100][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:49.101][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:49.102][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.103][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.104][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:49.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:49.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.108][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:49.109][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:49.110][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.111][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.112][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:49.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:49.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.116][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:49.117][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:49.118][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.119][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.120][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:49.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:49.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.124][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:49.125][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:49.126][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.126][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.128][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:49.129][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.130][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.131][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.132][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:49.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.136][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:49.137][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:49.138][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.138][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.140][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:49.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:49.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.143][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:49.144][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:49.145][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.146][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.148][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:49.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:49.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.152][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:49.153][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:49.154][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.155][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.156][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:49.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:49.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.160][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:49.161][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:49.162][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.162][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.164][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:49.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:49.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.168][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:49.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:49.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.172][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:49.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:49.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:49.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:49.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.180][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:49.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:49.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:49.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:49.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:49.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:49.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:49.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:49.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:49.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:49.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:49.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:49.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:49.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:49.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:49.207][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-09-05 23:05:49.208][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.212][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.215][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:49.241][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[2024-09-05 23:05:49.244][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-05 23:05:49.245][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-09-05 23:05:49.246][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:05:49.247][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-09-05 23:05:49.250][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:49.251][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:49.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:49.256][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:49.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:49.258][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:49.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:49.260][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.264][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.268][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:49.272][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:49.273][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:49.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:49.278][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:49.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:49.280][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:49.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:49.282][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.285][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.289][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.293][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.297][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:49.301][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:49.302][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:49.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:49.307][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:49.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:49.308][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:49.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:49.310][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.314][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.318][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.322][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.326][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:49.330][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:49.331][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:49.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:49.337][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:49.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:49.338][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:49.339][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.TRACE[2024-09-05 23:05:49.340][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.344][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.348][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.352][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.356][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:49.360][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:49.361][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:49.362][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:49.367][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:49.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:49.369][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:49.370][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.TRACE[2024-09-05 23:05:49.371][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.375][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.379][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:49.383][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:49.383][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:49.384][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:49.388][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:49.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:49.390][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:49.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:49.392][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.395][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.399][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:49.403][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:49.404][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:49.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:49.418][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:49.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:49.420][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:49.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:49.422][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.426][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.430][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:49.434][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:49.435][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:49.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:49.442][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:49.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:49.444][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:49.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:49.446][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.450][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.454][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:49.458][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:49.459][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:49.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:49.465][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:49.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:49.466][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:49.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:49.468][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.472][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.476][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:49.480][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:49.480][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:49.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:49.486][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:49.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:49.488][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:49.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:49.490][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.494][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.498][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:49.502][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:49.503][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:49.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:49.508][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:49.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:49.510][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:49.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:49.512][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.516][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.525][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:49.530][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:49.531][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:49.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:49.539][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:49.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:49.541][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:49.542][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.TRACE[2024-09-05 23:05:49.543][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.548][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.553][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:49.557][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:49.558][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:49.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:49.564][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:49.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:49.566][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:49.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:49.568][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.572][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.577][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:49.581][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:49.582][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:49.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:49.589][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:49.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:49.591][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:49.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:49.593][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.597][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.601][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:49.622][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:49.623][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:49.624][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:49.629][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:49.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:49.631][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:49.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:49.633][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.637][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.641][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:49.645][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:49.646][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:49.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:49.651][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:49.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:49.653][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:49.654][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.TRACE[2024-09-05 23:05:49.655][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.659][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.663][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:49.667][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:49.668][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:49.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:49.673][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:49.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:49.675][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:49.676][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.TRACE[2024-09-05 23:05:49.677][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.681][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.685][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:49.689][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:49.690][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:49.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:49.695][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:49.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:49.697][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:49.698][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.TRACE[2024-09-05 23:05:49.699][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.703][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.707][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:49.711][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:49.712][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:49.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:49.717][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:49.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:49.719][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:49.720][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[2024-09-05 23:05:49.721][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.725][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.729][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:49.733][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:49.733][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:49.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:49.738][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:49.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:49.740][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:49.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:49.742][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.746][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.749][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.765][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:49.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:49.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:49.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:49.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.772][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:49.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:49.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.776][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:49.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:49.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.779][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:49.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:49.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:49.813][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[2024-09-05 23:05:49.816][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-05 23:05:49.817][cch$loadFileContent] Trying to load 1 files from cache: [1]: "c5171beada848a87ef2ffa10427d9be3".
biodb.TRACE[2024-09-05 23:05:49.818][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:05:49.820][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content".
biodb.DEBUG[2024-09-05 23:05:49.823][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[2024-09-05 23:05:49.826][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-05 23:05:49.827][cch$loadFileContent] Trying to load 1 files from cache: [1]: "750e63ff76a843f016511fa71c89113e".
biodb.TRACE[2024-09-05 23:05:49.828][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:05:49.829][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content".
biodb.DEBUG[2024-09-05 23:05:49.832][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:49.832][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:49.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:49.838][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:49.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:49.839][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:49.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:49.841][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-09-05 23:05:49.842][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-05 23:05:49.844][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-09-05 23:05:49.845][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:05:49.847][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml".
biodb.DEBUG[2024-09-05 23:05:49.848][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-05 23:05:49.849][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-05 23:05:49.850][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-05 23:05:49.852][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:49.853][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:49.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:49.858][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:49.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:49.860][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:49.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:49.863][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:49.864][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:49.865][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.866][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:49.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:49.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.871][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:49.872][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:49.873][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.874][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.875][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:49.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:49.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.879][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:49.880][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:49.881][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.882][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.883][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:49.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:49.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.887][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:49.888][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:49.889][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.890][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.891][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:49.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:49.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.895][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:49.896][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:49.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.897][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.899][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:49.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:49.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.902][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:49.903][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:49.904][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.905][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.906][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:49.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:49.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.910][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:49.911][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.912][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.913][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.914][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:49.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:49.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.918][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:49.919][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:49.920][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.921][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.922][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:49.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:49.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.926][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:49.927][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:49.928][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.929][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.931][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:49.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:49.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.935][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:49.936][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:49.937][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.938][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.939][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:49.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:49.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.943][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:49.945][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:49.946][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.947][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.948][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:49.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:49.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.952][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:49.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:49.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.964][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:49.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:49.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:49.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:49.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.971][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:49.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:49.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:49.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:49.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.979][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:49.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:49.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:49.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:49.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:49.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:49.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:49.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:49.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:49.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:49.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:49.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:49.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:49.998][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-09-05 23:05:50.000][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.003][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.007][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:50.011][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:50.012][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:50.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:50.017][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:50.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:50.019][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:50.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:50.021][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.025][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.029][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:50.033][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:50.034][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:50.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:50.039][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:50.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:50.041][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:50.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:50.043][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-09-05 23:05:50.044][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-05 23:05:50.046][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-09-05 23:05:50.047][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:05:50.049][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml".
biodb.DEBUG[2024-09-05 23:05:50.050][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-05 23:05:50.051][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-05 23:05:50.052][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-05 23:05:50.054][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:50.055][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:50.056][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:50.061][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:50.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:50.063][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:50.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:50.067][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:50.068][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:50.069][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.070][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:50.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:50.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.076][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:50.077][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:50.078][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.078][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.080][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:50.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:50.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.084][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:50.085][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:50.086][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.087][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.088][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:50.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:50.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.092][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:50.093][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:50.094][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.095][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.096][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:50.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:50.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.100][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:50.101][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:50.102][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.103][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.104][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:50.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:50.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.109][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:50.110][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:50.111][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.112][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.113][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:50.114][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:50.115][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.116][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.117][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:50.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:50.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.121][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.122][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.123][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.124][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.125][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.129][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:50.130][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:50.131][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.132][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.140][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:50.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:50.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.144][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:50.145][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:50.146][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.147][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.148][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:50.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:50.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.153][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:50.154][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:50.155][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.156][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.157][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:50.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:50.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.162][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:50.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:50.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.166][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:50.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:50.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:50.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:50.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.173][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:50.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:50.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:50.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:50.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:50.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:50.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:50.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:50.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:50.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:50.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:50.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:50.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:50.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:50.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:50.201][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-09-05 23:05:50.203][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.206][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.210][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:50.233][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[2024-09-05 23:05:50.236][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-05 23:05:50.238][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-09-05 23:05:50.239][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:05:50.240][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-09-05 23:05:50.244][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:50.245][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:50.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:50.251][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:50.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:50.253][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:50.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:50.255][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.259][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.263][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:50.267][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:50.268][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:50.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:50.274][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:50.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:50.275][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:50.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:50.277][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.281][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.285][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.289][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.293][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:50.297][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:50.298][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:50.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:50.304][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:50.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:50.306][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:50.307][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[2024-09-05 23:05:50.308][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.312][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.316][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.329][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:50.337][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:50.338][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:50.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:50.343][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:50.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:50.345][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:50.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:50.347][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.351][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.355][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.359][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.362][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:50.366][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:50.367][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:50.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:50.372][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:50.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:50.374][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:50.375][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.TRACE[2024-09-05 23:05:50.376][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.380][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:50.387][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:50.388][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:50.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:50.393][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:50.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:50.395][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:50.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:50.397][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.400][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.404][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:50.408][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:50.409][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:50.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:50.414][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:50.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:50.415][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:50.416][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.TRACE[2024-09-05 23:05:50.417][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.421][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.425][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:50.429][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:50.429][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:50.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:50.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:50.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:50.436][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:50.437][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.TRACE[2024-09-05 23:05:50.439][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.443][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.446][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:50.450][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:50.451][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:50.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:50.456][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:50.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:50.458][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:50.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:50.460][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.464][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.467][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:50.471][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:50.472][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:50.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:50.477][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:50.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:50.479][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:50.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:50.481][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.485][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.496][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:50.501][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:50.502][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:50.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:50.507][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:50.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:50.509][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:50.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:50.511][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.515][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.519][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:50.523][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:50.523][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:50.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:50.529][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:50.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:50.531][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:50.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:50.533][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.537][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.540][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:50.544][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:50.545][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:50.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:50.550][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:50.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:50.552][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:50.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:50.554][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.558][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.561][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:50.565][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:50.566][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:50.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:50.571][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:50.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:50.573][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:50.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:50.575][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.578][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.582][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:50.586][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:50.586][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:50.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:50.591][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:50.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:50.593][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:50.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:50.595][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.599][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.603][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:50.607][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:50.607][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:50.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:50.613][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:50.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:50.614][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:50.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:50.616][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.620][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.624][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:50.628][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:50.628][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:50.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:50.634][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:50.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:50.635][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:50.636][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[2024-09-05 23:05:50.637][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.641][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.645][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:50.649][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:50.650][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:50.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:50.655][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:50.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:50.657][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:50.658][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[2024-09-05 23:05:50.659][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.670][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.673][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:50.677][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:50.678][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:50.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:50.684][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:50.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:50.685][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:50.686][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.TRACE[2024-09-05 23:05:50.687][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.691][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.695][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:50.699][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:50.699][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:50.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:50.705][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:50.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:50.706][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:50.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:50.708][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.712][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:50.716][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:50.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:50.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:50.735][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.INFO [2024-09-05 23:05:50.738][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.DEBUG[2024-09-05 23:05:50.739][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-05 23:05:50.740][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-05 23:05:50.742][private$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[2024-09-05 23:05:51.314][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[2024-09-05 23:05:51.866][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-05 23:05:51.868][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-09-05 23:05:51.872][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-09-05 23:05:51.876][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:51.877][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:51.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:51.882][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:51.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:51.884][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:51.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:51.886][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:51.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:51.890][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:51.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:51.894][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:51.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:51.897][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:51.898][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:51.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:51.903][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:51.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:51.905][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:51.906][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.TRACE[2024-09-05 23:05:51.907][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:51.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:51.910][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:51.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:51.914][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:51.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:51.918][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:51.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:51.922][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:51.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:51.925][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:51.926][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:51.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:51.931][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:51.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:51.933][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:51.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:51.935][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:51.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:51.939][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:51.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:51.942][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:51.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:51.946][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:51.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:51.950][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:51.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:51.962][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:51.963][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:51.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:51.968][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:51.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:51.970][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:51.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:51.971][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:51.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:51.975][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:51.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:51.979][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:51.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:51.983][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:51.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:51.986][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:51.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:51.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:51.990][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:51.991][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:51.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:51.996][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:51.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:51.997][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:51.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:51.999][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.003][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.007][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:52.010][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:52.011][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:52.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:52.016][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:52.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:52.018][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:52.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:52.020][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.023][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.027][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:52.031][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:52.032][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:52.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:52.037][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:52.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:52.039][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:52.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:52.041][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.045][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:52.052][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:52.053][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:52.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:52.058][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:52.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:52.060][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:52.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:52.062][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.065][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:52.073][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:52.074][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:52.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:52.079][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:52.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:52.080][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:52.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:52.082][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.086][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.090][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:52.093][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:52.094][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:52.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:52.099][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:52.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:52.101][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:52.101][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[2024-09-05 23:05:52.103][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.106][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.110][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:52.113][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:52.114][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:52.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:52.125][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:52.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:52.126][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:52.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:52.128][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.132][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.136][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:52.139][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:52.140][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:52.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:52.145][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:52.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:52.147][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:52.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:52.149][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.152][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.156][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:52.160][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:52.161][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:52.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:52.166][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:52.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:52.168][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:52.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:52.170][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.174][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.177][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:52.181][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:52.182][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:52.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:52.187][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:52.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:52.188][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:52.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:52.190][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.194][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.198][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:52.201][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:52.202][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:52.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:52.207][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:52.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:52.209][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:52.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:52.211][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.215][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.219][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:52.222][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:52.223][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:52.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:52.229][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:52.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:52.230][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:52.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:52.232][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.236][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.240][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:52.244][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:52.244][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:52.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:52.250][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:52.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:52.252][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:52.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:52.254][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.257][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.261][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:52.265][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:52.266][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:52.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:52.271][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:52.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:52.273][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:52.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:52.275][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.279][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.282][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:52.295][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:52.296][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:52.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:52.301][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:52.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:52.303][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:52.304][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.TRACE[2024-09-05 23:05:52.305][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.309][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.313][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:52.316][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:52.317][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:52.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:52.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:52.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:52.324][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:52.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:52.326][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.330][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:52.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.349][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-09-05 23:05:52.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-09-05 23:05:52.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-09-05 23:05:52.359][biodb::testThat]
biodb.INFO [2024-09-05 23:05:52.360][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-09-05 23:05:52.361][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-05 23:05:52.362][biodb::testThat]
biodb.TRACE[2024-09-05 23:05:52.364][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-05 23:05:52.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-05 23:05:52.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.368][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:52.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:52.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.372][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:52.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:52.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.375][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:52.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:52.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:52.379][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:52.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:52.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:52.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:52.385][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:52.386][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:52.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:52.391][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:52.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:52.393][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:52.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:52.396][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[2024-09-05 23:05:52.399][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-05 23:05:52.400][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-05 23:05:52.402][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-09-05 23:05:52.785][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-09-05 23:05:53.186][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2024-09-05 23:05:53.189][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-09-05 23:05:53.191][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-09-05 23:05:53.196][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-09-05 23:05:53.199][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:53.200][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:53.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:53.218][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:53.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:53.220][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:53.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:53.222][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:53.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:53.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:53.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:53.226][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:53.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:53.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:53.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:53.230][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:53.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:53.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:53.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:53.235][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[2024-09-05 23:05:53.239][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-05 23:05:53.240][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-05 23:05:53.241][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-09-05 23:05:53.628][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-09-05 23:05:54.031][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-05 23:05:54.034][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-09-05 23:05:54.038][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-09-05 23:05:54.041][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:54.042][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:54.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:54.047][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:54.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:54.049][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:54.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:54.051][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:54.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:54.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:54.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:54.055][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:54.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:54.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:54.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:54.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:54.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:54.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:54.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:54.063][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:54.064][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:54.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:54.069][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:54.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:54.071][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:54.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:54.073][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:54.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:54.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:54.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:54.077][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:54.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:54.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:54.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:54.081][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:54.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:54.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:54.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:54.085][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-09-05 23:05:54.087][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:54.088][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:54.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:54.093][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:54.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:54.095][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:54.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:54.097][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:54.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:54.101][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:54.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:54.105][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:54.106][private$selectFields]
biodb.TRACE[2024-09-05 23:05:54.107][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-05 23:05:54.108][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-05 23:05:54.109][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:54.110][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.111][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.112][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:54.112][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:54.114][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.115][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.116][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:54.116][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:54.117][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:54.118][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:54.119][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.120][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:54.122][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:54.123][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-05 23:05:54.124][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:54.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:54.128][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:54.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:54.132][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:54.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:54.146][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-09-05 23:05:54.147][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:54.148][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:54.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:54.153][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:54.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:54.155][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:54.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:54.157][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:54.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:54.160][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:54.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:54.164][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:54.165][private$selectFields]
biodb.TRACE[2024-09-05 23:05:54.166][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-05 23:05:54.167][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-05 23:05:54.168][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:54.169][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.170][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.170][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:54.171][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:54.172][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.173][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.174][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:54.175][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:54.176][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:54.177][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:54.178][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.179][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.180][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:54.180][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:54.181][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-05 23:05:54.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:54.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:54.186][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:54.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:54.190][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:54.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:54.194][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-09-05 23:05:54.195][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:54.195][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:54.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:54.206][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:54.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:54.208][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:54.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:54.210][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:54.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:54.214][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:54.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:54.218][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:54.219][private$selectFields]
biodb.TRACE[2024-09-05 23:05:54.219][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-05 23:05:54.220][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-05 23:05:54.221][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:54.222][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.223][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.224][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:54.225][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:54.226][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.227][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.228][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:54.229][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:54.230][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:54.231][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:54.232][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.233][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.234][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:54.235][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:54.236][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-05 23:05:54.237][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:54.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:54.241][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:54.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:54.244][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:54.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:54.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:54.248][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-09-05 23:05:54.249][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-09-05 23:05:54.250][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-09-05 23:05:54.259][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:54.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:54.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:54.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:54.263][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:54.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:54.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:54.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:54.267][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:54.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:54.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:54.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:54.271][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:54.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:54.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:54.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:54.326][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:54.327][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:54.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:54.332][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:54.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:54.334][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:54.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:54.337][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-05 23:05:54.341][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-05 23:05:54.341][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-05 23:05:54.343][private$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[2024-09-05 23:05:54.727][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[2024-09-05 23:05:55.116][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-05 23:05:55.119][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-09-05 23:05:55.138][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-09-05 23:05:55.144][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[2024-09-05 23:05:55.150][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-05 23:05:55.152][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-05 23:05:55.155][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-09-05 23:05:55.593][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-09-05 23:05:56.174][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-05 23:05:56.177][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-09-05 23:05:56.182][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-09-05 23:05:56.185][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:56.186][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:56.187][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:56.193][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:56.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:56.195][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:56.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:56.197][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.202][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.207][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:56.212][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:56.213][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:56.214][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:56.219][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:56.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:56.221][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:56.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:56.224][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.228][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.232][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:56.236][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:56.237][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:56.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:56.242][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:56.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:56.244][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:56.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:56.246][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.249][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.253][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:56.278][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-09-05 23:05:56.301][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:56.302][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:56.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:56.306][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:56.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:56.308][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:56.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:56.310][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.314][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.317][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:56.326][private$selectFields]
biodb.TRACE[2024-09-05 23:05:56.327][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-05 23:05:56.328][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-05 23:05:56.329][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:56.330][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.331][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.332][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.333][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.334][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.335][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.336][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.336][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.337][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:56.338][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:56.339][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.340][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.341][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.342][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.343][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-05 23:05:56.344][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.347][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.351][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.355][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-09-05 23:05:56.356][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:56.357][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:56.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:56.362][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:56.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:56.364][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:56.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:56.377][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.380][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.403][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:56.404][private$selectFields]
biodb.TRACE[2024-09-05 23:05:56.405][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-05 23:05:56.406][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-05 23:05:56.406][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:56.407][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.408][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.409][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.410][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.411][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.412][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.413][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.414][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.414][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:56.424][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:56.425][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.426][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.427][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.428][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.428][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-05 23:05:56.429][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.433][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.437][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.441][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-09-05 23:05:56.442][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:56.442][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:56.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:56.447][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:56.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:56.449][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:56.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:56.451][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.454][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.458][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:56.459][private$selectFields]
biodb.TRACE[2024-09-05 23:05:56.460][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-05 23:05:56.461][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-05 23:05:56.461][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:56.462][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.463][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.464][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.465][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.466][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.467][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.472][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.473][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.474][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:56.475][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:56.476][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.477][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.478][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.479][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.480][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-05 23:05:56.481][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.484][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.488][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.492][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-09-05 23:05:56.493][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-09-05 23:05:56.494][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-09-05 23:05:56.502][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-09-05 23:05:56.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-09-05 23:05:56.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-09-05 23:05:56.508][biodb::testThat]
biodb.INFO [2024-09-05 23:05:56.509][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-09-05 23:05:56.510][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-05 23:05:56.511][biodb::testThat]
biodb.TRACE[2024-09-05 23:05:56.513][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-05 23:05:56.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-05 23:05:56.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.517][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:56.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:56.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.521][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:56.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:56.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.524][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:56.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:56.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.528][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:56.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:56.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:56.533][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:56.534][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:56.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:56.539][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:56.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:56.541][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:56.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:56.544][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-05 23:05:56.547][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-05 23:05:56.548][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-09-05 23:05:56.549][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:05:56.550][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-09-05 23:05:56.553][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:56.553][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:56.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:56.558][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:56.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:56.560][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:56.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:56.562][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:56.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:56.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.565][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:56.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:56.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.569][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:56.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:56.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:56.573][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-05 23:05:56.576][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-05 23:05:56.577][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-09-05 23:05:56.578][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:05:56.580][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-09-05 23:05:56.582][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:56.582][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:56.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:56.587][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:56.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:56.589][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:56.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:56.591][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:56.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:56.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.595][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:56.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:56.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.598][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:56.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:56.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:56.602][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:56.603][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:56.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:56.608][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:56.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:56.609][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:56.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:56.611][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:56.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:56.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.615][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:56.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:56.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.619][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:56.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:56.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:56.622][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-09-05 23:05:56.624][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:56.625][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:56.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:56.630][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:56.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:56.637][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:56.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:56.639][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.643][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.647][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:56.648][private$selectFields]
biodb.TRACE[2024-09-05 23:05:56.649][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-05 23:05:56.650][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-05 23:05:56.650][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:56.651][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.652][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.653][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.654][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.655][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.656][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.657][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.658][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.659][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:56.660][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:56.661][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.662][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.662][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.663][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.664][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-05 23:05:56.665][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.669][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.672][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.676][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-09-05 23:05:56.677][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:56.678][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:56.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:56.683][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:56.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:56.685][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:56.686][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.TRACE[2024-09-05 23:05:56.687][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.690][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.694][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:56.695][private$selectFields]
biodb.TRACE[2024-09-05 23:05:56.696][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-05 23:05:56.696][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-05 23:05:56.697][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:56.698][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.699][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.700][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.701][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.702][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.703][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.704][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.704][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.705][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:56.706][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:56.707][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.708][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.709][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.710][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.711][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-05 23:05:56.712][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.715][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.719][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.723][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-09-05 23:05:56.724][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:56.725][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:56.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:56.730][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:56.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:56.731][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:56.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:56.733][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.737][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.740][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:56.741][private$selectFields]
biodb.TRACE[2024-09-05 23:05:56.742][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-05 23:05:56.743][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-05 23:05:56.744][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:56.745][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.746][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.747][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.747][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.748][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.749][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.750][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.751][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.752][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:56.753][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:56.754][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.755][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.755][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.756][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.757][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-05 23:05:56.758][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.762][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.765][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.769][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-09-05 23:05:56.770][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-09-05 23:05:56.771][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-09-05 23:05:56.779][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.782][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.786][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.794][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:56.801][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:56.801][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:56.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:56.806][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:56.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:56.808][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:56.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:56.811][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-05 23:05:56.814][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-05 23:05:56.816][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-09-05 23:05:56.817][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:05:56.818][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-09-05 23:05:56.821][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-05 23:05:56.824][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-05 23:05:56.825][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-09-05 23:05:56.826][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:05:56.827][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-09-05 23:05:56.829][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:56.830][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:56.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:56.835][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:56.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:56.837][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:56.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:56.839][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.842][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.846][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:56.850][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:56.850][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:56.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:56.856][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:56.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:56.857][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:56.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:56.859][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.863][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.867][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:56.870][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:56.871][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:56.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:56.876][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:56.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:56.878][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:56.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:56.880][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.883][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.887][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:56.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:56.891][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-09-05 23:05:56.892][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:56.893][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:56.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:56.898][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:56.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:56.900][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:56.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:56.902][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.905][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.909][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:56.910][private$selectFields]
biodb.TRACE[2024-09-05 23:05:56.911][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-05 23:05:56.912][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-05 23:05:56.913][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:56.914][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.914][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.915][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.916][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.917][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.918][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.919][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.920][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.921][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:56.922][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:56.923][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.924][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.924][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.925][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.926][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-05 23:05:56.927][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.931][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.935][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.939][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-09-05 23:05:56.940][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:56.940][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:56.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:56.946][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:56.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:56.947][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:56.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:56.949][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.958][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.962][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:56.963][private$selectFields]
biodb.TRACE[2024-09-05 23:05:56.964][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-05 23:05:56.965][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-05 23:05:56.966][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:56.967][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.968][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.969][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.969][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.970][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.971][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.973][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.974][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:56.975][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:56.976][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.977][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.978][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.979][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.979][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-05 23:05:56.980][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.984][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.988][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:56.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:56.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:56.992][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-09-05 23:05:56.993][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:56.993][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:56.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:56.998][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:56.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:57.000][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:57.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:57.002][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.006][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.009][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:57.010][private$selectFields]
biodb.TRACE[2024-09-05 23:05:57.011][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-05 23:05:57.012][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-05 23:05:57.013][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:57.014][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.014][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.015][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.016][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.017][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.018][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.019][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.020][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.021][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:57.021][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:57.022][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.023][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.024][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.025][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.026][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-05 23:05:57.027][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.030][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.034][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.038][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-09-05 23:05:57.039][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-09-05 23:05:57.040][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-09-05 23:05:57.047][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-09-05 23:05:57.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-09-05 23:05:57.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-09-05 23:05:57.053][biodb::testThat]
biodb.INFO [2024-09-05 23:05:57.054][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-09-05 23:05:57.055][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-05 23:05:57.056][biodb::testThat]
biodb.TRACE[2024-09-05 23:05:57.058][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-05 23:05:57.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-05 23:05:57.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.062][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:57.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:57.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.066][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:57.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:57.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.069][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:57.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:57.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.073][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:57.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:57.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:57.080][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:57.081][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:57.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:57.086][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:57.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:57.088][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:57.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:57.091][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-05 23:05:57.094][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-05 23:05:57.095][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-09-05 23:05:57.096][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:05:57.098][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-09-05 23:05:57.100][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:57.101][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:57.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:57.106][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:57.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:57.107][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:57.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:57.109][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:57.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:57.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.117][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:57.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:57.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.121][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:57.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:57.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:57.126][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-05 23:05:57.129][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-05 23:05:57.130][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-09-05 23:05:57.131][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:05:57.132][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-09-05 23:05:57.134][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:57.135][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:57.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:57.140][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:57.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:57.142][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:57.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:57.144][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:57.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:57.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.148][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:57.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:57.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.151][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:57.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:57.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:57.155][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:57.156][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:57.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:57.161][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:57.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:57.162][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:57.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:57.164][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:57.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:57.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.168][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:57.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:57.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.171][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:57.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:57.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:57.175][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-09-05 23:05:57.177][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:57.177][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:57.178][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:57.182][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:57.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:57.184][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:57.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:57.186][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.190][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.193][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:57.194][private$selectFields]
biodb.TRACE[2024-09-05 23:05:57.195][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-05 23:05:57.196][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-05 23:05:57.197][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:57.198][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.199][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.199][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.200][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.201][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.202][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.203][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.204][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.205][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:57.206][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:57.207][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.208][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.208][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.209][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.210][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-05 23:05:57.211][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.215][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.218][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.222][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-09-05 23:05:57.223][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:57.224][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:57.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:57.229][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:57.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:57.231][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:57.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:57.233][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.236][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.240][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:57.241][private$selectFields]
biodb.TRACE[2024-09-05 23:05:57.242][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-05 23:05:57.242][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-05 23:05:57.243][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:57.244][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.245][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.246][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.247][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.248][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.249][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.250][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.250][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.251][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:57.252][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:57.253][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.254][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.255][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.256][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.257][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-05 23:05:57.258][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.261][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.265][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.269][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-09-05 23:05:57.270][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:57.271][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:57.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:57.283][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:57.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:57.285][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:57.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:57.287][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.295][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.300][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:57.301][private$selectFields]
biodb.TRACE[2024-09-05 23:05:57.302][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-05 23:05:57.303][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-05 23:05:57.304][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:57.306][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.307][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.308][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.309][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.310][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.311][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.312][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.313][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.314][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:57.315][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:57.316][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.317][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.319][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.320][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-05 23:05:57.321][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.325][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.329][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.334][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-09-05 23:05:57.335][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-09-05 23:05:57.336][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-09-05 23:05:57.356][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:57.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:57.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.360][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:57.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:57.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.364][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:57.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:57.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.368][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:57.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:57.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:57.377][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:57.378][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:57.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:57.383][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:57.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:57.385][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:57.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:57.389][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-05 23:05:57.392][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-05 23:05:57.394][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-09-05 23:05:57.395][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:05:57.396][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-09-05 23:05:57.400][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-05 23:05:57.403][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-05 23:05:57.404][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-09-05 23:05:57.405][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:05:57.407][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-09-05 23:05:57.409][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:57.410][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:57.411][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:57.416][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:57.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:57.418][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:57.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:57.420][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:57.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:57.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.424][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:57.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:57.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.428][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:57.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:57.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:57.432][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:57.433][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:57.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:57.438][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:57.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:57.440][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:57.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:57.442][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:57.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:57.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.446][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:57.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:57.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.450][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:57.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:57.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:57.454][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:57.455][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:57.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:57.473][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:57.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:57.475][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:57.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:57.477][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:57.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:57.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.482][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:57.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:57.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.486][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:57.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:57.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:57.490][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-09-05 23:05:57.491][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:57.492][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:57.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:57.497][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:57.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:57.499][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:57.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:57.501][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.504][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.508][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:57.509][private$selectFields]
biodb.TRACE[2024-09-05 23:05:57.510][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-05 23:05:57.511][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-05 23:05:57.511][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:57.512][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.513][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.514][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.515][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.516][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.517][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.518][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.519][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.520][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:57.520][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:57.521][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.522][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.523][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.524][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.525][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-05 23:05:57.526][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.529][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.533][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.537][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-09-05 23:05:57.538][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:57.539][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:57.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:57.544][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:57.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:57.545][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:57.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:57.547][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.551][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.554][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:57.555][private$selectFields]
biodb.TRACE[2024-09-05 23:05:57.556][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-05 23:05:57.557][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-05 23:05:57.558][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:57.559][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.560][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.560][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.561][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.562][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.563][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.564][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.565][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.566][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:57.567][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:57.568][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.568][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.569][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.570][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.571][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-05 23:05:57.572][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.576][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.580][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.584][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-09-05 23:05:57.585][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:57.586][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:57.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:57.591][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:57.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:57.592][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:57.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:57.594][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.598][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.602][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:57.603][private$selectFields]
biodb.TRACE[2024-09-05 23:05:57.603][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-05 23:05:57.604][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-05 23:05:57.605][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:57.606][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.607][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.608][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.609][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.610][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.611][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.612][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.613][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.613][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:57.614][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-05 23:05:57.615][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.616][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.617][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.618][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.619][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-05 23:05:57.620][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.623][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.632][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:57.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:57.636][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-09-05 23:05:57.637][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-09-05 23:05:57.638][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-09-05 23:05:57.655][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-09-05 23:05:57.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-09-05 23:05:57.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:57.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-09-05 23:05:57.661][biodb::testThat]
biodb.INFO [2024-09-05 23:05:57.662][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2024-09-05 23:05:57.663][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-05 23:05:57.664][biodb::testThat]
biodb.DEBUG[2024-09-05 23:05:57.665][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-09-05 23:05:57.666][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-05 23:05:57.668][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-09-05 23:05:57.669][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-05 23:05:57.670][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-05 23:05:57.671][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-05 23:05:57.672][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-05 23:05:57.673][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-05 23:05:57.674][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-05 23:05:57.676][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:57.677][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:57.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:57.682][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:57.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:57.683][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:57.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:57.685][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-09-05 23:05:57.688][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-05 23:05:57.689][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-05 23:05:57.690][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-09-05 23:05:58.077][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-09-05 23:05:58.489][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-05 23:05:58.494][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-09-05 23:05:58.501][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-09-05 23:05:58.506][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-09-05 23:05:58.509][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-05 23:05:58.511][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-05 23:05:58.514][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-05 23:05:58.517][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:58.519][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:58.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:58.530][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:58.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:58.534][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:58.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:05:58.539][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:58.541][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:58.543][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:58.544][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:58.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:58.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:58.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:58.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:58.552][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:05:58.553][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:05:58.555][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:58.556][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:58.557][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:05:58.559][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:05:58.560][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:58.561][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:58.563][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:05:58.564][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:05:58.565][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:58.566][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:58.567][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:05:58.569][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:05:58.570][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:58.571][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:58.572][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:58.573][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:05:58.574][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:58.575][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:58.576][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:05:58.577][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:05:58.578][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:58.579][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:58.580][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:58.581][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:05:58.582][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:58.583][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:58.584][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:05:58.585][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:05:58.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:58.587][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:58.588][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:05:58.589][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:05:58.590][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:58.591][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:58.592][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:05:58.593][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:05:58.594][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:58.595][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:58.596][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:58.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:58.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:58.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:58.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:58.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:58.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:58.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:58.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:58.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:58.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:58.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:58.607][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:05:58.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:05:58.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:58.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:58.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:58.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:58.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:58.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:58.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:58.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:58.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:58.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:58.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:58.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:58.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:58.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:58.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:58.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:58.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:58.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:58.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:58.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:58.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:58.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:05:58.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:05:58.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:05:58.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:05:58.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:05:58.640][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-09-05 23:05:58.641][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-09-05 23:05:58.648][biodb::testThat]
biodb.INFO [2024-09-05 23:05:58.649][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-09-05 23:05:58.650][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-05 23:05:58.651][biodb::testThat]
biodb.DEBUG[2024-09-05 23:05:58.659][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-09-05 23:05:58.660][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-09-05 23:05:58.660][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-09-05 23:05:58.662][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-09-05 23:05:58.663][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2024-09-05 23:05:58.664][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-05 23:05:58.665][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-05 23:05:58.666][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-05 23:05:58.667][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-05 23:05:58.668][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-05 23:05:58.671][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:58.672][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:58.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:58.677][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:58.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:58.679][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:58.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:58.681][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2024-09-05 23:05:58.683][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-05 23:05:58.684][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-05 23:05:58.685][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-09-05 23:05:59.072][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-09-05 23:05:59.464][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-05 23:05:59.466][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-09-05 23:05:59.469][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-09-05 23:05:59.470][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:05:59.471][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:05:59.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:05:59.476][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:05:59.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:05:59.478][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:05:59.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:05:59.480][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2024-09-05 23:05:59.483][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-05 23:05:59.484][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-05 23:05:59.485][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2024-09-05 23:05:59.875][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2024-09-05 23:06:00.273][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-05 23:06:00.276][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2024-09-05 23:06:00.280][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2024-09-05 23:06:00.281][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:06:00.282][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:00.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:00.289][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:00.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:00.291][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:00.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:00.293][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2024-09-05 23:06:00.296][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-05 23:06:00.297][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-05 23:06:00.298][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-09-05 23:06:00.682][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2024-09-05 23:06:01.078][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-05 23:06:01.082][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-09-05 23:06:01.089][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-09-05 23:06:01.094][private$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[2024-09-05 23:06:01.097][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-05 23:06:01.099][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-09-05 23:06:01.102][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-09-05 23:06:01.105][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:06:01.107][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:01.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:01.117][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:01.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:01.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:01.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:06:01.127][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:01.129][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:01.131][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.132][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:01.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:01.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.139][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:06:01.141][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:06:01.142][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.143][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.145][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:06:01.146][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:06:01.147][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.148][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.150][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:06:01.151][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:06:01.152][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.153][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.155][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:06:01.156][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:06:01.157][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.158][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.159][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:06:01.160][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:06:01.161][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.162][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.163][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:06:01.186][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:06:01.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.189][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.191][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:06:01.192][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:06:01.193][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.194][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.195][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:06:01.196][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:06:01.197][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.198][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.199][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:06:01.200][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:06:01.201][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.202][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.203][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:06:01.204][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:06:01.205][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.206][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.208][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:06:01.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:06:01.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.211][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:06:01.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:06:01.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:01.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:01.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.219][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:06:01.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:06:01.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:01.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:01.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:01.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:01.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:01.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:01.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:06:01.235][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:06:01.236][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:01.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:01.241][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:01.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:01.243][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:01.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:06:01.246][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:01.247][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:01.247][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.248][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:01.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:01.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.253][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:06:01.254][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:06:01.255][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.256][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.258][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:06:01.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:06:01.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.261][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:06:01.262][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:06:01.263][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.264][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.266][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:06:01.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:06:01.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.270][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:06:01.271][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:06:01.271][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.272][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.273][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:06:01.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:06:01.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.277][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:06:01.278][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:06:01.279][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.280][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.281][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:06:01.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:06:01.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.285][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:06:01.286][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:06:01.287][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.287][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.288][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:06:01.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:06:01.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.292][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:06:01.293][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:06:01.294][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.295][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.296][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:06:01.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:06:01.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.300][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:06:01.301][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:06:01.302][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.302][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.304][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:06:01.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:06:01.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.307][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:06:01.308][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:06:01.309][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.310][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.311][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:06:01.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:06:01.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.315][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:06:01.316][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:06:01.317][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.318][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.319][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:06:01.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:06:01.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.322][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:06:01.323][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:06:01.324][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.325][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.326][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:06:01.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:06:01.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.330][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:06:01.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:06:01.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.333][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:06:01.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:06:01.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:01.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:01.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.341][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:06:01.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:06:01.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:01.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:01.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:01.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:01.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:01.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:01.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:06:01.361][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:06:01.362][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:01.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:01.367][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:01.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:01.369][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:01.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-05 23:06:01.372][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:01.373][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:01.373][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.374][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:01.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:01.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.379][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:06:01.380][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:06:01.381][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.382][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.383][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:06:01.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:06:01.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.387][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:06:01.388][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:06:01.389][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.389][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.391][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:06:01.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:06:01.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.394][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:06:01.395][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:06:01.396][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.397][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.398][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:06:01.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:06:01.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.402][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:06:01.402][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:06:01.403][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.404][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.405][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:06:01.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:06:01.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.409][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:06:01.410][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:06:01.411][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.412][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.413][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:06:01.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:06:01.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.416][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:06:01.417][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:06:01.418][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.419][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.420][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:06:01.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:06:01.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.424][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:06:01.425][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:06:01.426][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.426][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.428][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:06:01.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:06:01.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.431][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:06:01.432][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:06:01.433][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.434][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.435][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:06:01.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:06:01.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.439][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:06:01.440][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:06:01.441][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.441][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.442][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:06:01.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:06:01.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.446][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:06:01.447][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:06:01.448][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.449][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.450][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:06:01.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:06:01.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.454][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:06:01.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:06:01.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.457][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:06:01.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:06:01.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:01.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:01.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.465][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:06:01.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:06:01.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:01.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:01.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.472][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:01.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:01.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:01.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:01.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:01.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:01.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.483][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:01.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:01.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:01.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:01.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:01.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:01.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:01.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:01.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:01.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:01.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:01.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:01.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:01.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:01.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:01.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:01.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:01.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:01.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:06:01.517][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-09-05 23:06:01.518][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-09-05 23:06:01.519][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-09-05 23:06:01.530][biodb::testThat]
biodb.INFO [2024-09-05 23:06:01.531][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2024-09-05 23:06:01.532][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-05 23:06:01.532][biodb::testThat]
biodb.INFO [2024-09-05 23:06:01.553][biodb::testThat]
biodb.INFO [2024-09-05 23:06:01.554][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2024-09-05 23:06:01.555][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-05 23:06:01.556][biodb::testThat]
biodb.INFO [2024-09-05 23:06:01.562][biodb::testThat]
biodb.INFO [2024-09-05 23:06:01.563][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2024-09-05 23:06:01.564][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-05 23:06:01.565][biodb::testThat]
biodb.DEBUG[2024-09-05 23:06:01.567][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2024-09-05 23:06:01.570][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-05 23:06:01.571][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-05 23:06:01.573][private$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[2024-09-05 23:06:02.047][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[2024-09-05 23:06:02.655][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-05 23:06:02.659][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-09-05 23:06:02.666][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-09-05 23:06:02.679][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:06:02.680][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:06:02.681][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:02.682][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:02.683][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:06:02.684][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:06:02.685][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:02.686][ef$get] fields variable is a list.
biodb.INFO [2024-09-05 23:06:02.688][biodb::testThat]
biodb.INFO [2024-09-05 23:06:02.689][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2024-09-05 23:06:02.690][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-05 23:06:02.691][biodb::testThat]
biodb.ERROR[2024-09-05 23:06:02.707][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-09-05 23:06:02.725][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-09-05 23:06:02.738][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-09-05 23:06:02.740][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-09-05 23:06:02.741][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-09-05 23:06:02.742][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-09-05 23:06:02.743][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:02.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:02.744][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:02.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:02.746][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:02.747][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.INFO [2024-09-05 23:06:02.768][biodb::testContext]
biodb.INFO [2024-09-05 23:06:02.770][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-05 23:06:02.770][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-09-05 23:06:02.771][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-05 23:06:02.772][biodb::testContext]
biodb.INFO [2024-09-05 23:06:02.774][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-09-05 23:06:02.776][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-09-05 23:06:02.781][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-05 23:06:02.782][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-09-05 23:06:02.783][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-09-05 23:06:02.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:02.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:02.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:02.787][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-09-05 23:06:02.788][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-09-05 23:06:02.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:02.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:02.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:02.792][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-09-05 23:06:02.793][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-09-05 23:06:02.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:02.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:02.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:02.796][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-09-05 23:06:02.798][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-09-05 23:06:02.799][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-09-05 23:06:02.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:02.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:02.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:02.802][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-09-05 23:06:02.803][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-09-05 23:06:02.804][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-09-05 23:06:02.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:02.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:02.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:02.808][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-09-05 23:06:02.809][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-09-05 23:06:02.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:02.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:02.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:02.813][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-09-05 23:06:02.814][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-09-05 23:06:02.815][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-09-05 23:06:02.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:02.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:02.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:02.818][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-09-05 23:06:02.819][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-09-05 23:06:02.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:02.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:02.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:02.823][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-09-05 23:06:02.824][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-09-05 23:06:02.825][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-09-05 23:06:02.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:02.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:02.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:02.829][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-09-05 23:06:02.830][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-09-05 23:06:02.831][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-09-05 23:06:02.832][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-09-05 23:06:02.833][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-09-05 23:06:02.834][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-09-05 23:06:02.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:02.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:02.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:02.837][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-09-05 23:06:02.838][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-09-05 23:06:02.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:02.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:02.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:02.842][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-09-05 23:06:02.843][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-09-05 23:06:02.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:02.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:02.846][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[2024-09-05 23:06:02.847][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-09-05 23:06:02.848][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-09-05 23:06:02.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:02.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:02.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:02.857][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-09-05 23:06:02.859][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-09-05 23:06:02.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:02.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:02.862][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[2024-09-05 23:06:02.863][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-09-05 23:06:02.865][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-09-05 23:06:02.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:02.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:02.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:02.869][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-09-05 23:06:02.870][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-09-05 23:06:02.873][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-09-05 23:06:02.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:02.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:02.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:02.877][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-09-05 23:06:02.878][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-09-05 23:06:02.879][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-09-05 23:06:02.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:02.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:02.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:02.883][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-09-05 23:06:02.886][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:02.887][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-09-05 23:06:02.888][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:02.889][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-05 23:06:02.890][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:02.891][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-05 23:06:02.892][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:02.893][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-05 23:06:02.895][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-05 23:06:02.896][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-05 23:06:02.897][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:02.898][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-09-05 23:06:02.899][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-05 23:06:02.900][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:02.901][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:02.902][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-05 23:06:02.902][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-05 23:06:02.902][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-05 23:06:02.902][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-05 23:06:02.902][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-05 23:06:02.903][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-05 23:06:02.904][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:06:02.905][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:06:02.906][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-05 23:06:02.907][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:06:02.908][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:06:02.909][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-05 23:06:02.910][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:02.912][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-05 23:06:02.913][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-05 23:06:02.914][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:02.915][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:02.916][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-09-05 23:06:02.918][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:02.920][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-09-05 23:06:02.921][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:02.922][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-05 23:06:02.923][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:02.924][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-05 23:06:02.925][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:02.926][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-05 23:06:02.927][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-05 23:06:02.929][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-05 23:06:02.930][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:02.931][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-09-05 23:06:02.932][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-05 23:06:02.933][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:02.934][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:02.935][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-05 23:06:02.935][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-05 23:06:02.935][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-05 23:06:02.935][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-05 23:06:02.935][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-05 23:06:02.936][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-05 23:06:02.937][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:06:02.938][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:06:02.939][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-05 23:06:02.940][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:06:02.941][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:06:02.942][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-05 23:06:02.944][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:02.966][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-05 23:06:02.968][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-05 23:06:02.970][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:02.971][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:02.972][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-09-05 23:06:02.974][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:02.976][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-09-05 23:06:02.977][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:02.978][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-05 23:06:02.979][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:02.980][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-05 23:06:02.981][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:02.982][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-05 23:06:02.983][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-05 23:06:02.984][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-05 23:06:02.986][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:02.987][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-09-05 23:06:02.988][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-05 23:06:02.989][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:02.990][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:02.991][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:02.992][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-05 23:06:02.993][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:06:02.994][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:06:02.995][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-05 23:06:02.996][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:06:02.997][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:06:02.998][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-05 23:06:02.999][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:03.000][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-05 23:06:03.001][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-05 23:06:03.002][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:03.003][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:03.005][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-09-05 23:06:03.007][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:03.008][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-09-05 23:06:03.009][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:03.010][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-05 23:06:03.011][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:03.012][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-05 23:06:03.013][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:03.015][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-05 23:06:03.016][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-05 23:06:03.017][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-05 23:06:03.018][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:03.019][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-09-05 23:06:03.020][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-05 23:06:03.021][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:03.022][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:03.023][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:03.024][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-05 23:06:03.026][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:06:03.026][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:06:03.028][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-05 23:06:03.029][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:06:03.029][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:06:03.030][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-05 23:06:03.032][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:03.033][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-05 23:06:03.034][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-05 23:06:03.035][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:03.036][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:03.037][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-05 23:06:03.038][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.039][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[2024-09-05 23:06:03.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:03.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:03.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:03.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:03.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:03.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:03.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:03.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:03.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:03.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:03.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:03.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:03.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:03.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.071][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[2024-09-05 23:06:03.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:03.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:03.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:03.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:03.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:03.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.083][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[2024-09-05 23:06:03.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:03.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:03.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:03.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:03.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:03.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.096][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[2024-09-05 23:06:03.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:03.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.100][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[2024-09-05 23:06:03.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:03.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:03.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:03.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:03.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:03.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.112][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[2024-09-05 23:06:03.113][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-09-05 23:06:03.115][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-09-05 23:06:03.116][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-09-05 23:06:03.117][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-09-05 23:06:03.119][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-09-05 23:06:03.120][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-09-05 23:06:03.121][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-09-05 23:06:03.122][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-09-05 23:06:03.124][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-09-05 23:06:03.125][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-09-05 23:06:03.126][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-05 23:06:03.128][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-09-05 23:06:03.135][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-09-05 23:06:03.137][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-09-05 23:06:03.139][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-09-05 23:06:03.140][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-09-05 23:06:03.141][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-09-05 23:06:03.143][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-09-05 23:06:03.144][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-09-05 23:06:03.145][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-09-05 23:06:03.146][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-09-05 23:06:03.148][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-09-05 23:06:03.149][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-09-05 23:06:03.150][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-09-05 23:06:03.152][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-09-05 23:06:03.153][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-09-05 23:06:03.154][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-09-05 23:06:03.156][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-09-05 23:06:03.157][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-09-05 23:06:03.158][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-09-05 23:06:03.159][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-09-05 23:06:03.161][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-09-05 23:06:03.162][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-09-05 23:06:03.163][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-09-05 23:06:03.164][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-09-05 23:06:03.166][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-09-05 23:06:03.167][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-09-05 23:06:03.168][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-09-05 23:06:03.170][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-09-05 23:06:03.171][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-09-05 23:06:03.172][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-09-05 23:06:03.173][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-09-05 23:06:03.175][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-09-05 23:06:03.176][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-09-05 23:06:03.177][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-09-05 23:06:03.179][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-09-05 23:06:03.180][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-09-05 23:06:03.181][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-09-05 23:06:03.182][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-09-05 23:06:03.184][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-09-05 23:06:03.185][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-09-05 23:06:03.186][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-09-05 23:06:03.188][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-09-05 23:06:03.189][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-09-05 23:06:03.190][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-09-05 23:06:03.191][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-09-05 23:06:03.193][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-09-05 23:06:03.194][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-09-05 23:06:03.195][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-09-05 23:06:03.196][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-09-05 23:06:03.198][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-09-05 23:06:03.199][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-09-05 23:06:03.200][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-09-05 23:06:03.202][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-09-05 23:06:03.203][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-09-05 23:06:03.204][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-09-05 23:06:03.205][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-09-05 23:06:03.207][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-09-05 23:06:03.208][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-09-05 23:06:03.209][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-09-05 23:06:03.210][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-09-05 23:06:03.212][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-09-05 23:06:03.213][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-09-05 23:06:03.214][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-09-05 23:06:03.216][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-09-05 23:06:03.217][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-09-05 23:06:03.218][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-09-05 23:06:03.220][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-09-05 23:06:03.221][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-09-05 23:06:03.222][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-09-05 23:06:03.224][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-09-05 23:06:03.225][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-09-05 23:06:03.226][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-09-05 23:06:03.228][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-09-05 23:06:03.229][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-09-05 23:06:03.230][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-05 23:06:03.231][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.233][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:03.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:03.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:03.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:03.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:03.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:03.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:03.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:03.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:03.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:03.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:03.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:03.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:03.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:03.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:03.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:03.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:03.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:03.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:03.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:03.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:03.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:03.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:03.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:03.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:03.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:03.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:03.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:03.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:03.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:03.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:03.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:03.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:03.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:03.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:03.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:03.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:03.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:03.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:03.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:03.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:03.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:03.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:03.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:03.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:03.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:03.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:03.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:03.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:03.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:03.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:03.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:03.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:03.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:03.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:03.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:03.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.323][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[2024-09-05 23:06:03.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:03.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:03.326][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:03.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:03.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:03.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:03.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:03.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.335][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[2024-09-05 23:06:03.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:03.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:03.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:03.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:03.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:03.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:03.341][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[2024-09-05 23:06:03.342][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-09-05 23:06:03.344][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-09-05 23:06:03.346][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:03.347][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-09-05 23:06:03.347][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:03.348][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-05 23:06:03.349][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:03.350][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-05 23:06:03.351][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:03.352][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-09-05 23:06:03.353][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-09-05 23:06:03.354][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-05 23:06:03.355][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:03.356][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-09-05 23:06:03.357][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-05 23:06:03.358][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-09-05 23:06:03.358][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-09-05 23:06:03.358][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-09-05 23:06:03.358][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-09-05 23:06:03.358][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-09-05 23:06:03.358][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-09-05 23:06:03.358][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-09-05 23:06:03.358][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-09-05 23:06:03.358][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-09-05 23:06:03.358][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-09-05 23:06:03.358][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-09-05 23:06:03.359][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:03.360][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-05 23:06:03.360][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-05 23:06:03.360][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-05 23:06:03.361][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-09-05 23:06:03.362][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:06:03.363][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:06:03.363][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-05 23:06:03.364][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:06:03.365][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:06:03.366][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-05 23:06:03.367][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-05 23:06:03.367][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-09-05 23:06:03.368][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-05 23:06:03.369][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-05 23:06:03.370][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:03.371][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-09-05 23:06:03.371][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-09-05 23:06:03.372][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-09-05 23:06:03.374][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-05 23:06:03.375][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-09-05 23:06:03.376][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-09-05 23:06:03.378][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-09-05 23:06:03.380][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-09-05 23:06:03.383][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-09-05 23:06:03.385][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-09-05 23:06:03.386][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-09-05 23:06:03.388][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-09-05 23:06:03.389][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-05 23:06:03.390][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-05 23:06:03.391][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-09-05 23:06:03.392][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-09-05 23:06:03.394][biodb::testThat]
biodb.INFO [2024-09-05 23:06:03.395][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2024-09-05 23:06:03.396][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-05 23:06:03.397][biodb::testThat]
biodb.DEBUG[2024-09-05 23:06:03.401][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-09-05 23:06:03.404][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-05 23:06:03.405][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-05 23:06:03.407][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2024-09-05 23:06:03.816][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2024-09-05 23:06:04.355][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-05 23:06:04.357][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2024-09-05 23:06:04.361][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2024-09-05 23:06:04.365][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-09-05 23:06:04.368][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-05 23:06:04.369][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-05 23:06:04.371][private$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[2024-09-05 23:06:04.756][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[2024-09-05 23:06:05.164][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-05 23:06:05.168][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2024-09-05 23:06:05.175][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2024-09-05 23:06:05.178][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:06:05.180][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:05.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:05.189][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:05.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:05.192][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:05.194][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[2024-09-05 23:06:05.431][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[2024-09-05 23:06:05.442][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-05 23:06:05.443][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-05 23:06:05.445][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-09-05 23:06:05.867][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-09-05 23:06:06.289][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-05 23:06:06.291][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2024-09-05 23:06:06.295][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2024-09-05 23:06:06.297][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:06:06.298][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:06.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:06.303][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:06.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:06.304][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:06.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:06.320][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:06:06.321][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:06.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:06.326][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:06.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:06.328][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:06.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:06.333][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-09-05 23:06:06.336][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-05 23:06:06.337][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-09-05 23:06:06.339][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:06:06.340][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-09-05 23:06:06.341][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:06:06.342][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:06.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:06.347][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:06.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:06.348][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:06.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:06.351][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-09-05 23:06:06.354][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-05 23:06:06.355][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-09-05 23:06:06.356][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:06:06.357][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-09-05 23:06:06.359][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:06:06.359][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:06.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:06.364][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:06.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:06.366][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:06.367][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[2024-09-05 23:06:06.368][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:06:06.369][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:06.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:06.374][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:06.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:06.375][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:06.376][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[2024-09-05 23:06:06.380][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-09-05 23:06:06.383][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-05 23:06:06.384][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-09-05 23:06:06.385][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:06:06.386][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-09-05 23:06:06.388][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:06:06.388][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:06.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:06.393][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:06.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:06.395][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:06.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:06.397][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-09-05 23:06:06.400][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-05 23:06:06.402][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-09-05 23:06:06.403][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:06:06.404][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-09-05 23:06:06.406][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:06:06.407][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:06.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:06.412][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:06.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:06.414][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:06.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:06.417][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-09-05 23:06:06.420][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-05 23:06:06.421][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-05 23:06:06.423][private$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[2024-09-05 23:06:06.811][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[2024-09-05 23:06:07.207][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-05 23:06:07.212][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2024-09-05 23:06:07.220][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2024-09-05 23:06:07.224][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:06:07.226][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:07.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:07.238][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:07.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:07.242][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:07.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-09-05 23:06:07.256][biodb::testThat]
biodb.INFO [2024-09-05 23:06:07.258][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2024-09-05 23:06:07.260][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-05 23:06:07.262][biodb::testThat]
biodb.DEBUG[2024-09-05 23:06:07.267][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[2024-09-05 23:06:07.272][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-05 23:06:07.274][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-05 23:06:07.278][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-09-05 23:06:07.679][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-09-05 23:06:08.072][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-05 23:06:08.074][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-09-05 23:06:08.078][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-09-05 23:06:08.080][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:06:08.081][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:08.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:08.086][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:08.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:08.088][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:08.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:08.093][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-09-05 23:06:08.096][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-05 23:06:08.097][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-05 23:06:08.099][private$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[2024-09-05 23:06:08.487][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[2024-09-05 23:06:08.919][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-05 23:06:08.924][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-09-05 23:06:08.933][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-09-05 23:06:08.946][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:06:08.950][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:08.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:08.966][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:08.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:08.970][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:08.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-09-05 23:06:08.981][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-09-05 23:06:08.983][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-09-05 23:06:08.985][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-09-05 23:06:08.986][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-09-05 23:06:08.988][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:08.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:08.990][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:08.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:08.993][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:08.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-09-05 23:06:08.999][biodb::testContext]
biodb.INFO [2024-09-05 23:06:09.000][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-05 23:06:09.002][biodb::testContext] Test context - Test web services
biodb.INFO [2024-09-05 23:06:09.003][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-05 23:06:09.004][biodb::testContext]
biodb.INFO [2024-09-05 23:06:09.007][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-09-05 23:06:09.009][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-09-05 23:06:09.013][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-05 23:06:09.014][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-09-05 23:06:09.015][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-09-05 23:06:09.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.019][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-09-05 23:06:09.020][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-09-05 23:06:09.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.024][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-09-05 23:06:09.025][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-09-05 23:06:09.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.029][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-09-05 23:06:09.030][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-09-05 23:06:09.031][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-09-05 23:06:09.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.033][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[2024-09-05 23:06:09.034][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-09-05 23:06:09.035][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-09-05 23:06:09.037][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-09-05 23:06:09.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.040][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-09-05 23:06:09.041][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-09-05 23:06:09.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.045][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-09-05 23:06:09.046][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-09-05 23:06:09.047][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-09-05 23:06:09.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.051][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-09-05 23:06:09.052][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-09-05 23:06:09.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.056][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-09-05 23:06:09.057][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-09-05 23:06:09.058][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-09-05 23:06:09.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.061][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-09-05 23:06:09.062][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-09-05 23:06:09.064][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-09-05 23:06:09.079][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-09-05 23:06:09.092][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-09-05 23:06:09.093][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-09-05 23:06:09.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.096][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[2024-09-05 23:06:09.097][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-09-05 23:06:09.098][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-09-05 23:06:09.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.101][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-09-05 23:06:09.102][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-09-05 23:06:09.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.105][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[2024-09-05 23:06:09.106][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-09-05 23:06:09.107][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-09-05 23:06:09.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.110][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-09-05 23:06:09.111][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-09-05 23:06:09.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.115][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-09-05 23:06:09.116][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-09-05 23:06:09.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.120][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-09-05 23:06:09.121][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-09-05 23:06:09.125][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-09-05 23:06:09.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.128][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[2024-09-05 23:06:09.129][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-09-05 23:06:09.130][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-09-05 23:06:09.131][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-09-05 23:06:09.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.135][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-09-05 23:06:09.136][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:09.137][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-09-05 23:06:09.138][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:09.139][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-05 23:06:09.140][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:09.141][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-05 23:06:09.142][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:09.143][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-05 23:06:09.144][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-05 23:06:09.145][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-05 23:06:09.146][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:09.147][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-09-05 23:06:09.148][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-05 23:06:09.149][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:09.150][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:09.151][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-05 23:06:09.151][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-05 23:06:09.151][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-05 23:06:09.151][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-05 23:06:09.151][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-05 23:06:09.152][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-05 23:06:09.153][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:06:09.154][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:06:09.155][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-05 23:06:09.156][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:06:09.156][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:06:09.157][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-05 23:06:09.158][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:09.159][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-05 23:06:09.160][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-05 23:06:09.161][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:09.162][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:09.163][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-09-05 23:06:09.165][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:09.166][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-09-05 23:06:09.167][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:09.168][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-05 23:06:09.169][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:09.170][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-05 23:06:09.171][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:09.171][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-05 23:06:09.172][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-05 23:06:09.173][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-05 23:06:09.174][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:09.175][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-09-05 23:06:09.176][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-05 23:06:09.177][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:09.178][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:09.179][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-05 23:06:09.179][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-05 23:06:09.179][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-05 23:06:09.179][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-05 23:06:09.179][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-05 23:06:09.180][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-05 23:06:09.181][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:06:09.182][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:06:09.183][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-05 23:06:09.184][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:06:09.185][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:06:09.186][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-05 23:06:09.186][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:09.187][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-05 23:06:09.188][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-05 23:06:09.189][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:09.190][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:09.191][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-09-05 23:06:09.193][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:09.194][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-09-05 23:06:09.195][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:09.196][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-05 23:06:09.197][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:09.198][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-05 23:06:09.199][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:09.200][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-05 23:06:09.201][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-05 23:06:09.202][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-05 23:06:09.203][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:09.203][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-09-05 23:06:09.204][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-05 23:06:09.205][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:09.206][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:09.207][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:09.208][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-05 23:06:09.209][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:06:09.210][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:06:09.211][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-05 23:06:09.212][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:06:09.213][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:06:09.214][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-05 23:06:09.215][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:09.216][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-05 23:06:09.217][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-05 23:06:09.218][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:09.219][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:09.220][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-09-05 23:06:09.222][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:09.223][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-09-05 23:06:09.224][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:09.225][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-05 23:06:09.226][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:09.227][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-05 23:06:09.228][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:09.229][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-05 23:06:09.230][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-05 23:06:09.231][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-05 23:06:09.232][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:09.232][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-09-05 23:06:09.233][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-05 23:06:09.234][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:09.235][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:09.236][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:09.237][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-05 23:06:09.238][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:06:09.239][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:06:09.240][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-05 23:06:09.241][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:06:09.242][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:06:09.243][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-05 23:06:09.244][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:09.245][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-05 23:06:09.245][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-05 23:06:09.246][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:09.247][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:09.249][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-05 23:06:09.250][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.325][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-09-05 23:06:09.326][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-09-05 23:06:09.327][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-09-05 23:06:09.329][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-09-05 23:06:09.330][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-09-05 23:06:09.331][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-09-05 23:06:09.332][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-09-05 23:06:09.334][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-09-05 23:06:09.335][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-09-05 23:06:09.336][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-09-05 23:06:09.338][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-05 23:06:09.339][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-09-05 23:06:09.340][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-09-05 23:06:09.341][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-09-05 23:06:09.343][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-09-05 23:06:09.344][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-09-05 23:06:09.345][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-09-05 23:06:09.346][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-09-05 23:06:09.348][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-09-05 23:06:09.349][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-09-05 23:06:09.350][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-09-05 23:06:09.351][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-09-05 23:06:09.353][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-09-05 23:06:09.354][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-09-05 23:06:09.355][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-09-05 23:06:09.356][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-09-05 23:06:09.358][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-09-05 23:06:09.359][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-09-05 23:06:09.360][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-09-05 23:06:09.362][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-09-05 23:06:09.363][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-09-05 23:06:09.364][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-09-05 23:06:09.365][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-09-05 23:06:09.367][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-09-05 23:06:09.368][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-09-05 23:06:09.369][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-09-05 23:06:09.370][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-09-05 23:06:09.372][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-09-05 23:06:09.373][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-09-05 23:06:09.374][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-09-05 23:06:09.375][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-09-05 23:06:09.377][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-09-05 23:06:09.378][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-09-05 23:06:09.379][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-09-05 23:06:09.380][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-09-05 23:06:09.382][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-09-05 23:06:09.383][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-09-05 23:06:09.384][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-09-05 23:06:09.390][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-09-05 23:06:09.391][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-09-05 23:06:09.393][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-09-05 23:06:09.394][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-09-05 23:06:09.395][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-09-05 23:06:09.396][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-09-05 23:06:09.398][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-09-05 23:06:09.399][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-09-05 23:06:09.400][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-09-05 23:06:09.401][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-09-05 23:06:09.402][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-09-05 23:06:09.404][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-09-05 23:06:09.405][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-09-05 23:06:09.406][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-09-05 23:06:09.407][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-09-05 23:06:09.409][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-09-05 23:06:09.410][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-09-05 23:06:09.411][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-09-05 23:06:09.412][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-09-05 23:06:09.413][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-09-05 23:06:09.415][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-09-05 23:06:09.416][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-09-05 23:06:09.417][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-09-05 23:06:09.418][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-09-05 23:06:09.420][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-09-05 23:06:09.421][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-09-05 23:06:09.422][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-09-05 23:06:09.423][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-09-05 23:06:09.424][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-09-05 23:06:09.426][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-09-05 23:06:09.427][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-09-05 23:06:09.428][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-09-05 23:06:09.429][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-09-05 23:06:09.430][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-09-05 23:06:09.432][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-09-05 23:06:09.433][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-09-05 23:06:09.435][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-09-05 23:06:09.435][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-05 23:06:09.436][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.438][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:09.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:09.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:09.446][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:09.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:09.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:09.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.455][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[2024-09-05 23:06:09.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:09.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:09.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:09.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:09.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.466][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[2024-09-05 23:06:09.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:09.469][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:09.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:09.474][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:09.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:09.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:09.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.486][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[2024-09-05 23:06:09.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:09.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:09.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.495][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[2024-09-05 23:06:09.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:09.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:09.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:09.507][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:09.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:09.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:09.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.518][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[2024-09-05 23:06:09.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:09.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:09.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.525][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[2024-09-05 23:06:09.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:09.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:09.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:09.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:09.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:09.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:09.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.544][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.DEBUG[2024-09-05 23:06:09.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:09.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:09.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:09.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:09.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:09.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:09.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:09.551][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-09-05 23:06:09.552][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-09-05 23:06:09.554][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:09.555][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-09-05 23:06:09.556][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:09.557][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-05 23:06:09.557][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:09.558][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-05 23:06:09.559][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:09.560][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-09-05 23:06:09.561][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-09-05 23:06:09.562][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-05 23:06:09.563][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:09.564][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-09-05 23:06:09.565][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-05 23:06:09.566][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-09-05 23:06:09.566][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-09-05 23:06:09.566][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-09-05 23:06:09.566][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-09-05 23:06:09.566][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-09-05 23:06:09.566][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-09-05 23:06:09.566][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-09-05 23:06:09.566][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-09-05 23:06:09.566][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-09-05 23:06:09.566][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-09-05 23:06:09.566][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-09-05 23:06:09.567][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:09.568][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-05 23:06:09.568][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-05 23:06:09.568][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-05 23:06:09.568][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-09-05 23:06:09.569][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:06:09.570][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:06:09.571][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-05 23:06:09.572][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:06:09.573][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:06:09.574][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-05 23:06:09.574][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-05 23:06:09.574][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-09-05 23:06:09.575][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-05 23:06:09.576][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-05 23:06:09.577][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:09.578][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-09-05 23:06:09.578][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-09-05 23:06:09.579][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-09-05 23:06:09.581][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-05 23:06:09.582][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-09-05 23:06:09.583][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-09-05 23:06:09.585][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-09-05 23:06:09.586][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-09-05 23:06:09.589][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-09-05 23:06:09.590][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-09-05 23:06:09.591][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-09-05 23:06:09.593][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-09-05 23:06:09.594][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-05 23:06:09.595][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-05 23:06:09.596][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-09-05 23:06:09.597][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-09-05 23:06:09.599][biodb::testThat]
biodb.INFO [2024-09-05 23:06:09.599][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-09-05 23:06:09.600][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-05 23:06:09.601][biodb::testThat]
biodb.DEBUG[2024-09-05 23:06:09.604][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-09-05 23:06:09.608][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-05 23:06:09.609][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-09-05 23:06:09.611][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:06:09.612][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-09-05 23:06:09.615][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[2024-09-05 23:06:09.618][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-05 23:06:09.619][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-05 23:06:09.621][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-09-05 23:06:10.028][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-09-05 23:06:10.415][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-05 23:06:10.417][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-09-05 23:06:10.420][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-09-05 23:06:10.428][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-09-05 23:06:10.429][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-09-05 23:06:10.430][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-09-05 23:06:10.431][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-09-05 23:06:10.432][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:10.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:10.433][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.435][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-09-05 23:06:10.439][biodb::testContext]
biodb.INFO [2024-09-05 23:06:10.440][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-05 23:06:10.441][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-09-05 23:06:10.442][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-05 23:06:10.443][biodb::testContext]
biodb.INFO [2024-09-05 23:06:10.444][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-09-05 23:06:10.446][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-09-05 23:06:10.450][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-05 23:06:10.451][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-09-05 23:06:10.452][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-09-05 23:06:10.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.454][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[2024-09-05 23:06:10.455][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-09-05 23:06:10.456][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-09-05 23:06:10.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.460][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-09-05 23:06:10.460][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-09-05 23:06:10.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.464][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-09-05 23:06:10.465][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-09-05 23:06:10.466][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-09-05 23:06:10.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.469][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-09-05 23:06:10.470][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-09-05 23:06:10.471][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-09-05 23:06:10.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.474][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[2024-09-05 23:06:10.474][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-09-05 23:06:10.475][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-09-05 23:06:10.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.479][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-09-05 23:06:10.485][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-09-05 23:06:10.489][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-09-05 23:06:10.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.492][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-09-05 23:06:10.493][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-09-05 23:06:10.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.496][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-09-05 23:06:10.497][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-09-05 23:06:10.498][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-09-05 23:06:10.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.501][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-09-05 23:06:10.502][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-09-05 23:06:10.502][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-09-05 23:06:10.503][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-09-05 23:06:10.504][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-09-05 23:06:10.505][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-09-05 23:06:10.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.508][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-09-05 23:06:10.509][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-09-05 23:06:10.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.512][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-09-05 23:06:10.513][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-09-05 23:06:10.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.516][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-09-05 23:06:10.517][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-09-05 23:06:10.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.520][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-09-05 23:06:10.521][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-09-05 23:06:10.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.524][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-09-05 23:06:10.525][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-09-05 23:06:10.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.529][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-09-05 23:06:10.529][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-09-05 23:06:10.532][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-09-05 23:06:10.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.536][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-09-05 23:06:10.536][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-09-05 23:06:10.537][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-09-05 23:06:10.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.541][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-09-05 23:06:10.542][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:10.543][self$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[2024-09-05 23:06:10.544][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:10.545][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-05 23:06:10.546][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:10.547][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-05 23:06:10.547][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:10.548][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-05 23:06:10.549][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-05 23:06:10.550][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-05 23:06:10.551][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:10.552][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-09-05 23:06:10.553][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-05 23:06:10.553][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:10.554][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:10.555][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-05 23:06:10.555][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-05 23:06:10.555][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-05 23:06:10.555][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-05 23:06:10.555][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-05 23:06:10.556][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-05 23:06:10.557][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:06:10.558][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:06:10.559][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-05 23:06:10.559][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:06:10.560][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:06:10.561][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-05 23:06:10.562][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:10.563][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-05 23:06:10.563][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-05 23:06:10.564][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:10.565][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:10.566][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-09-05 23:06:10.568][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:10.569][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-09-05 23:06:10.569][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:10.570][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-05 23:06:10.571][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:10.572][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-05 23:06:10.573][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:10.574][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-05 23:06:10.575][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-05 23:06:10.576][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-05 23:06:10.576][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:10.577][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-09-05 23:06:10.578][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-05 23:06:10.579][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:10.580][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:10.581][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-05 23:06:10.581][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-05 23:06:10.581][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-05 23:06:10.581][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-05 23:06:10.581][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-05 23:06:10.582][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-05 23:06:10.583][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:06:10.583][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:06:10.584][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-05 23:06:10.585][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:06:10.586][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:06:10.587][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-05 23:06:10.587][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:10.588][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-05 23:06:10.589][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-05 23:06:10.590][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:10.591][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:10.592][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-09-05 23:06:10.593][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:10.594][self$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[2024-09-05 23:06:10.595][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:10.596][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-05 23:06:10.597][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:10.598][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-05 23:06:10.599][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:10.600][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-05 23:06:10.600][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-05 23:06:10.601][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-05 23:06:10.602][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:10.603][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-09-05 23:06:10.604][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-05 23:06:10.605][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:10.606][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:10.607][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:10.608][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-05 23:06:10.608][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:06:10.609][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:06:10.610][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-05 23:06:10.611][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:06:10.612][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:06:10.613][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-05 23:06:10.614][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:10.614][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-05 23:06:10.615][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-05 23:06:10.616][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:10.617][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:10.618][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-09-05 23:06:10.620][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:10.620][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-09-05 23:06:10.621][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:10.622][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-05 23:06:10.623][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:10.624][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-05 23:06:10.625][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:10.626][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-05 23:06:10.627][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-05 23:06:10.628][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-05 23:06:10.628][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:10.629][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-09-05 23:06:10.630][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-05 23:06:10.631][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:10.632][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:10.633][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:10.634][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-05 23:06:10.635][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:06:10.635][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:06:10.636][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-05 23:06:10.637][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:06:10.638][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:06:10.639][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-05 23:06:10.640][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:10.640][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-05 23:06:10.641][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-05 23:06:10.642][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:10.643][self$setPropertyValue]
biodb.DEBUG[2024-09-05 23:06:10.644][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-05 23:06:10.645][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.654][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[2024-09-05 23:06:10.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.662][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[2024-09-05 23:06:10.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.666][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[2024-09-05 23:06:10.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.686][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[2024-09-05 23:06:10.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.690][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[2024-09-05 23:06:10.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.694][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[2024-09-05 23:06:10.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.698][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[2024-09-05 23:06:10.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.702][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[2024-09-05 23:06:10.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.715][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-09-05 23:06:10.716][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-09-05 23:06:10.718][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-09-05 23:06:10.719][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-09-05 23:06:10.720][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-09-05 23:06:10.722][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-09-05 23:06:10.723][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-09-05 23:06:10.724][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-09-05 23:06:10.725][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-09-05 23:06:10.727][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-09-05 23:06:10.728][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-05 23:06:10.729][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-09-05 23:06:10.730][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-09-05 23:06:10.732][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-09-05 23:06:10.733][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-09-05 23:06:10.734][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-09-05 23:06:10.736][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-09-05 23:06:10.737][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-09-05 23:06:10.738][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-09-05 23:06:10.739][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-09-05 23:06:10.741][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-09-05 23:06:10.742][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-09-05 23:06:10.743][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-09-05 23:06:10.744][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-09-05 23:06:10.746][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-09-05 23:06:10.747][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-09-05 23:06:10.748][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-09-05 23:06:10.750][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-09-05 23:06:10.751][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-09-05 23:06:10.752][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-09-05 23:06:10.753][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-09-05 23:06:10.755][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-09-05 23:06:10.756][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-09-05 23:06:10.762][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-09-05 23:06:10.763][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-09-05 23:06:10.764][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-09-05 23:06:10.765][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-09-05 23:06:10.766][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-09-05 23:06:10.768][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-09-05 23:06:10.769][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-09-05 23:06:10.770][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-09-05 23:06:10.771][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-09-05 23:06:10.773][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-09-05 23:06:10.774][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-09-05 23:06:10.775][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-09-05 23:06:10.776][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-09-05 23:06:10.778][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-09-05 23:06:10.779][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-09-05 23:06:10.780][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-09-05 23:06:10.781][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-09-05 23:06:10.782][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-09-05 23:06:10.784][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-09-05 23:06:10.785][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-09-05 23:06:10.786][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-09-05 23:06:10.787][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-09-05 23:06:10.789][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-09-05 23:06:10.790][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-09-05 23:06:10.791][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-09-05 23:06:10.792][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-09-05 23:06:10.793][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-09-05 23:06:10.795][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-09-05 23:06:10.796][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-09-05 23:06:10.797][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-09-05 23:06:10.798][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-09-05 23:06:10.800][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-09-05 23:06:10.801][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-09-05 23:06:10.802][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-09-05 23:06:10.803][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-09-05 23:06:10.804][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-09-05 23:06:10.806][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-09-05 23:06:10.807][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-09-05 23:06:10.808][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-09-05 23:06:10.809][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-09-05 23:06:10.810][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-09-05 23:06:10.812][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-09-05 23:06:10.813][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-09-05 23:06:10.814][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-09-05 23:06:10.815][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-09-05 23:06:10.816][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-09-05 23:06:10.818][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-09-05 23:06:10.819][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-09-05 23:06:10.820][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-09-05 23:06:10.821][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-09-05 23:06:10.823][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-09-05 23:06:10.824][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-09-05 23:06:10.825][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-05 23:06:10.826][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.827][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:10.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:10.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:10.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:10.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:10.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:10.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:10.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:10.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.850][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[2024-09-05 23:06:10.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:10.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:10.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:10.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:10.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.860][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[2024-09-05 23:06:10.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:10.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:10.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.866][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[2024-09-05 23:06:10.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:10.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:10.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:10.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:10.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:10.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:10.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.883][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[2024-09-05 23:06:10.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:10.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:10.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:10.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:10.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.894][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[2024-09-05 23:06:10.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:10.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:10.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:10.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:10.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:10.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:10.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:10.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.910][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[2024-09-05 23:06:10.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:10.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:10.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.916][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[2024-09-05 23:06:10.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-05 23:06:10.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:10.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:10.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:10.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:10.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:10.921][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[2024-09-05 23:06:10.923][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-09-05 23:06:10.924][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-09-05 23:06:10.926][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:10.927][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-09-05 23:06:10.928][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:10.929][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-05 23:06:10.930][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:10.931][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-05 23:06:10.931][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:10.932][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-09-05 23:06:10.933][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-09-05 23:06:10.934][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-05 23:06:10.935][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:10.936][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-09-05 23:06:10.937][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-05 23:06:10.938][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-09-05 23:06:10.938][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-09-05 23:06:10.938][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-09-05 23:06:10.938][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-09-05 23:06:10.938][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-09-05 23:06:10.938][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-09-05 23:06:10.938][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-09-05 23:06:10.938][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-09-05 23:06:10.938][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-09-05 23:06:10.938][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-09-05 23:06:10.938][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-09-05 23:06:10.939][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-09-05 23:06:10.940][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-05 23:06:10.940][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-05 23:06:10.940][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-05 23:06:10.941][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-09-05 23:06:10.941][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:06:10.942][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:06:10.943][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-05 23:06:10.944][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-05 23:06:10.945][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-05 23:06:10.946][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-05 23:06:10.946][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-05 23:06:10.946][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-09-05 23:06:10.947][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-05 23:06:10.948][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-05 23:06:10.949][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-09-05 23:06:10.950][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-09-05 23:06:10.950][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-09-05 23:06:10.951][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-09-05 23:06:10.953][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-05 23:06:10.954][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-09-05 23:06:10.955][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-09-05 23:06:10.957][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-09-05 23:06:10.958][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-09-05 23:06:10.961][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-09-05 23:06:10.962][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-09-05 23:06:10.963][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-09-05 23:06:10.964][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-09-05 23:06:10.965][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-05 23:06:10.966][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-05 23:06:10.967][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-09-05 23:06:10.968][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-09-05 23:06:10.970][biodb::testThat]
biodb.INFO [2024-09-05 23:06:10.970][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-09-05 23:06:10.971][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-05 23:06:10.972][biodb::testThat]
biodb.DEBUG[2024-09-05 23:06:10.975][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-09-05 23:06:10.978][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-05 23:06:10.980][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-09-05 23:06:10.981][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:06:10.982][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-09-05 23:06:10.985][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-09-05 23:06:10.988][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-05 23:06:10.989][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-09-05 23:06:10.990][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-05 23:06:10.991][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-09-05 23:06:10.995][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-09-05 23:06:10.996][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-05 23:06:10.997][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-09-05 23:06:10.998][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-05 23:06:10.999][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-05 23:06:11.000][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-05 23:06:11.001][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-05 23:06:11.002][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-05 23:06:11.003][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-05 23:06:11.005][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:06:11.006][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:11.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:11.011][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:11.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:11.012][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:11.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-05 23:06:11.014][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-09-05 23:06:11.017][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-05 23:06:11.018][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-05 23:06:11.019][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-09-05 23:06:11.407][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2024-09-05 23:06:12.535][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-05 23:06:12.538][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-09-05 23:06:12.546][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-09-05 23:06:12.549][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-09-05 23:06:12.551][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-05 23:06:12.553][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-05 23:06:12.555][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-05 23:06:12.564][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-05 23:06:12.570][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:12.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:12.577][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:12.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:12.579][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:12.581][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[2024-09-05 23:06:12.586][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:12.587][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:12.588][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:12.589][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:12.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:12.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:12.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:12.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:12.594][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:06:12.595][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:06:12.596][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:12.597][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:12.599][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-05 23:06:12.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-05 23:06:12.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:12.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:12.602][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:06:12.603][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:06:12.604][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:12.605][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:12.607][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-05 23:06:12.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-05 23:06:12.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:12.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:12.616][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-05 23:06:12.617][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-05 23:06:12.618][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:12.619][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:12.622][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-05 23:06:12.623][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-05 23:06:12.624][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:12.625][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:12.626][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:06:12.627][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:06:12.628][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:12.629][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:12.631][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:06:12.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-05 23:06:12.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:12.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:12.635][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:06:12.636][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:06:12.637][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:12.638][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:12.639][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-05 23:06:12.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-05 23:06:12.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:12.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:12.643][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:06:12.644][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:06:12.645][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:12.646][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:12.648][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:06:12.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-05 23:06:12.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:12.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:12.652][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:06:12.653][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:06:12.654][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:12.655][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:12.657][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-05 23:06:12.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-05 23:06:12.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:12.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:12.661][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:06:12.662][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:06:12.663][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:12.664][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:12.665][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-05 23:06:12.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-05 23:06:12.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:12.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:12.669][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:06:12.670][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:06:12.671][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:12.672][ef$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:12.674][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-05 23:06:12.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-05 23:06:12.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:12.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:12.678][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:06:12.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:06:12.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:12.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:12.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:06:12.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:06:12.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:12.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:12.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:12.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:12.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:12.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:12.689][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-05 23:06:12.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-05 23:06:12.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:12.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:12.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:12.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:12.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:12.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:12.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:12.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:12.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:12.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:12.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:12.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:12.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:12.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:12.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:12.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:12.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:12.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:12.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:12.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:12.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:12.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-05 23:06:12.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-05 23:06:12.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-05 23:06:12.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-05 23:06:12.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-05 23:06:12.717][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-09-05 23:06:12.722][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-09-05 23:06:12.723][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-09-05 23:06:12.725][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-09-05 23:06:12.726][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-09-05 23:06:12.727][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-05 23:06:12.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-05 23:06:12.728][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-05 23:06:12.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-05 23:06:12.730][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-09-05 23:06:12.731][FUN] Functions in observer 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 375 ]
>
> proc.time()
user system elapsed
20.425 0.915 45.113
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 0.946 | 0.051 | 2.150 | |
| ChebiEntry | 0.135 | 0.000 | 0.135 | |